A quite hypothetical plan for three weeks in June in Italy

I was tempted to go to Spain (Madrid, Toledo, Sevilla, Cordoba, Granada) but Spain seems to get much hotter much earlier in the summer, and I tend to wilt in the heat so I'm leaning toward central/NW Italy.

I'll mention there is so much more to Spain than just the southern half of our country 😉

Have you considered northern Spain aka "Green Spain"? It's quite the contrast compared to the south of the country, and looks more like Ireland mixed in with the Alps. The weather is much more temperate, average is around 18-22C (60-70F) for June. From medieval villages, to the picturesque wine regions, the emerald waters of Bay of Biscay, the culinary delights of the Basque country, the Celtic culture of Galicia, and finally the towering jagged peaks of the Picos de Europa; Northern Spain has something for everyone and is generally less touristy than the rest of the country.

Here are few more reasons why you should consider the north of Spain: https://theculturetrip.com/europe/spain/articles/15-reasons-to-visit-green-spain-at-least-once-in-your-lifetime/

It looks well thought out particularly for an energetic 30something.
Some additions if inside activities become limited
Rome - The Palantine Hills with its accompanying buildings ...or just the gardens (near the Forum)
Rome - Villa d'Este in Tivoli
Rome - Appian Way
Florence - Pitti Palace and Boboli Gardens
You could add a day from Milan to Rome if any of my suggestions catch your interest.
Have you seen the recent post here about the 'new and improved' Uffizi? I think the article mentioned it would open later this month.
Some might think Lucca to be a prettier sleep spot than Pisa and it still links to CT

My 2 cents … I'd skip Pisa and Genoa add one of the Lakes - Como or Maggiorie would be my choices
Arezzo is just a town... Modena or Parma if you want to take "food" tours - if you are into cars … Ferrari and Lamborghini Museums
Too many days in Milan but you could venture into the Piemonte region if you like wine. I thought Turin was only worth a day.
I'd spend more time in the hill towns around Tuscany - many as cute a Siena. Siena at night is magical

Hi zaraem, in Rome I suggest sleeping in Trastevere that’s a picturesque bohemian district. The Santa Maria del Popolo sits in Rome’s oldest square and is a must see.
Buy your tickets for the Uffizi when you purchase your plane tickets and book your lodging. The Uffizi sells out at least two months prior of the date you’ll visit. I would skip Arezzo and Modena.
In the Cinque Terre I would visit Vernazza that requires a change in La Spezia Centrale train station taking a total of 1h 30m.
You’ll like Siena more if you spend the night rather than as a day trip from Florence. I would also take a direct train from Milan to Varenna on Lake Como (1h 15m) and take Rick Steves’ self-guided walking tour. Afterwards ferry over to Bellagio. Lake Como offers very dramatic scenery where mountains meet the lake.

Ahhh, I'll think about it! I've been to Barcelona, Tarragona, and Montserrat. I had planned a bunch of trips during lockdown and thought to use one of those (Madrid south into Andalusia, Balkans/Eastern Europe, central/NW Italy) but exploring Santiago de Compostela, Burgos, Bilbao, San Sebastian is seriously tempting...

Although I'm sure the ferry gives good views of the Cinque Terre, there is rail service to all five towns, so you don't have to take a ferry to get to any of them.

I haven't been to Lake Orta; I'm sure it's at least "nice". But my impression from reading comments here and there is that it isn't as interesting as Lake Maggiore (the Borromean Isles off shore near Stresa are lovely) or Lake Como (which probably has the best scenery of all the lakes).

I like your pacing.

Although I'm sure the ferry gives good views of the Cinque Terre,
there is rail service to all five towns, so you don't have to take a
ferry to get to any of them.

True. You do not have to take a boat to Manarola from Monterosso, nor would I take a train from Manarola backwards to Vernazza, if first arriving in Monterosso, on a one-day visit. You also don't "need" to go back to Monterosso to get a train to Pisa. You can, however, take a train all the way to Monterosso - the most northern of the 5 villages - and then work your way further south via all train, train + boat, or mostly boat, except for Corniglia 'cause the ferries don't service that one.

You can also do much more than just one of the little villages on a day trip: they are REALLY little! Still, if the day comes for your day trip and it's pouring rain, I'd abort the mission.

You haven't mentioned interest in hiking within Cinque Terre National Park? That's also an option, depending on weather, your physical ability, and which trails might be open when you visit. For instance, we've hiked from Monterosso to Vernazza and onward to Corniglia, and Manarola to Riomaggiore but some of those routes will not/may not be open when you go.

http://www.parconazionale5terre.it/Eindex.php

While you mentioned that you have already been to Rome and Florence, it doesn't sound like the prior experience with either was optimal due to the heat? I really think you are shorting both of them, with only 2 days for Rome and 1.5 for Florence. Given your to-do list of museums, cemeteries and churches (you sound like me!!!) I'd rethink the day trip from Florence. Pisa? I might rethink that one too.

Editing to add: Nancy does have a point about spending a night in Pisa to see Piazza dei Miracoli during uncrowded hours + explore some of the other landmarks. I just don't know as I'd make it a base for 3 nights.

In Rome, the Appian Way is a great place to walk outdoors in a peaceful and natural setting very close to the city.
Instead of Pisa, you might make Lucca your base town for that time. It’s a quick bus ride or train to Pisa and also the Cinque Terre. And the city has a lovely park that is on the walls that surround the old town, so a great place to stroll and eat/drink outside. It feels a bit calmer than Pisa.
Varenna is an easy train ride from Milan for a visit to Lake Como area.
Enjoy your trip!

Glad you like cemeteries --- you're planning to see three of our favorites. Spent most of a day in the one in Milan and didn't see it all. The one in Genoa had the horizontal surfaces of its huge white sculptures covered in thick gray dust which made for some dramatic photos. I hope they don't clean it all up before you get there --- it looked like several years' worth. The sculptures in the one in Rome are not creepy or fantastic or melodramatic or unintentionally funny like the others, it's just a quiet and lovely and lonely place. Well, OK, there might be a very very sad angel or two.

Check out the car museum (it's far more than just a bunch of cars being displayed) and the Egyptian museum in Torino (we especially liked the 2nd floor walkway around the walls of the main room --- there are cases exhibiting hundreds of the same artifact all lined up and making interesting patterns).

Too bad you are not food-oriented --- we would go back to Genoa and Camogli just to eat.

People will advise you not to stay in Pisa or spend so much time there, and we have never been there but we have a list of things to see in and really near Pisa, mostly churches and medieval buildings and art, so we plan to stay in the town. I'm pretty sure that it's only by staying in the town that you can see the buildings in the Piazza dei Miracoli without the crowds at dawn and dusk.

Haha, don't get me wrong -- I do love good food. I just don't plan my travels around it and when I'm traveling alone -- as I probably will be this time -- I tend to go to cafes or get takeaway instead of going to sit-down restaurants and lingering over a meal.

Love the suggestion of Varenna and the Appian Way, and I'm thinking I might do Pisa as a day trip from Florence (and Cinque Terre from Genoa) to minimize moving from hotel to hotel.

Ok, so you might like Sa Pesta in Genoa --- casual, could be quick if you want it to be, kind of like indoor streetfood. Farinata and savory tarts (we ate an assortment of these).

That sounds perfect, thanks!

There's some well-meaning but confusing direction going on here.

First off:

I would add Monterosso al Mare and is where the train will drop you
off. You will then need to take a boat to Manarola. From Manarola take
the train to Vernazza. You’ll also need to take the train back to
Monterosso to get back to Pisa...

As I'd mentioned above, if you take a ferry from Monterosso to Manarola you miss Vernazza and would have to backtrack to do that village. The order of villages from north to south are Monterosso, Vernazza, Corniglia (no ferry service to that one), Manarola and Riomaggiore. If using the Cinque Terre Treno card to get around the region by train (not that you have to but can be a nice time/money-saving convenience) add Levanto on the far northern end, and La Spezia on the southern end. La Spezia is a very frequent gateway for trains from Florence and some other places into the region. Pisa is another one but I'd look at either option depending on your point of departure.

https://www.cinqueterre.eu.com/en/cinque-terre-card

Anyway, that's why the suggestion to take a ferry from a southernly to a northernly point - e.g. La Spezia or Riomaggiore to Monterosso - and then work your way back south through some of the other villages via trains. This is a great website for transport and other info on the region, although I'd give it some time to get up to speed for when Italy's open again.

https://www.apathtolunch.com/2014/06/complete-cinque-terre-portovenere-la.html

Another vote for a ramble on the Appia Antica (Rome). To date, that was our favorite day in Rome: a LONG one on foot, as we started so far out, but there was so much to see! Happy that you've added it to your list; here's the official website for the park:

https://www.parcoappiaantica.it

There are a couple of downloadable guides - in English! - on this page:

https://www.parcoappiaantica.it/home/risorse-e-utilita/download/category/1-flyer

The first one the list (AppiaAnticaeng2015.pdf) is the most helpful if trekking stretches of the road. Not all of the ticketed attractions along the way, such as the catacombs, are open every day of the week, and most are still closed to COVID so reference their hours closer to your trip.

I didn't read all responses so hope Im not repeating too much:
We (active family of 5 - 3 teens) spent 3 weeks in N. Spain in 2019 and LOVED it. We flew in to Barcelona and headed directly to Girona for the first two days. Rented a car there and drove, almost directly to San Seb (stopped at a castle en route, and after doing the drive I want to return and explore much more surrounding that route). From SS we drove to Bilbao. Bilbao to Llanes, but there are so many towns along that coast to choose from - too many for our three weeks. From Llanes we went into the Picos de Europa - took the cable at Feunte De and hiked, spent a little time in Potes, then headed to the western side of the picos to hike to the basilica and the lakes outside of Covadonga (all of it was stunning). From the Congas de Onis area we went to Oviedo, then headed back to the coast and visited cathedral beach (stayed in a B&B on the coast for a night because it was en route and affordable that turned out to be a gem). From cathedral beach to Santiago de Compostela, then to Léon, then Burgos, then Zaragoza, and ended in BCN, where we returned the car and stayed for several days. We all loved all of it. So beautiful. We've also done a trip similar to what you describe (and I would definitely hike the trails in the Cinque Terre instead of taking a ferry!), and the northern Spain trip was beautiful in a different way. It felt very different than the rest of Spain, more like Switzerland (and yes, the Picos are called the other Swiss Alps), not because you are in the mountains necessarily, nit the mountain range really separates the northern part of Spain from the rest so that you feel like you are in a very different country. Its much less populated, and the culture is different (because of the Basque influence but also I think, because of the geographic separation). You're going from San Seb with its rich Basque culture to Santiago de Compostela which reminded me of Portugal.
Anyway, that's my plug for Northern Spain ;)

Our favorite sight in Milan was The Last Supper. It had timed entries so it was easy to see and fit in with other things that day.

On hot days, museums may not be more pleasant places to be then outside.

Not sure but I don't think Uffizi or Accademia are air-conditioned. Plus those venues are likely to be full of people. Churches can be cool inside even on hot days.

But it sounds like the OP prioritizes the cultural institutions so can't really argue with the choices.

Val d'Orcia near Siena has glorious landscapes. So do most of Tuscany but a car makes it easier. I've been to San Miniato a couple of times, never went inside, but went there for the views of Florence from there.

Cinque Terre is not a day trip, though there are all-day tours out of Florence. But that area is about hiking, as are towns like Portofino, Camogli, Santa Margherita Ligure.

Similarly, Lake Como, while close to Milan, is really not a day trip, though I suppose you can train up to Como and take a around-trip hydrofoil to Bellagio. There are glorious villas all around the lake though, with beautiful gardens set against the lake. But hard to do that in a day trip out of Milan.