90 day trip to Italy in 3 years. Just starting the fun.

1. Malta - ferry or plane from Catania.
2. Consider a base in Bologna. The train connections are excellent.
3. We are going to Milano (6 days) and Varenna (Lake Como, 3 days) in early March. It will be our first time in those places. PM me in April and ask me what I think.
4. Treviso is wonderful for 3-4 days.
5. Can I come with you? I will ask my wife if it is OK.

I know you are probably aware of the 90 day Schengen visa restrictions. Make sure you absolutely positively do not overstay.

You have seen some beautiful parts of Italy already, especially Liguria.
Have fun planning this portion.

Re: Bari. We planned a trip to Puglia and Sicily last year. Getting from Bari to Palermo or Catania was going to require a flight from Bari to Rome with a layover and another flight to Sicily. Around 4.5 hours. Then I discovered Volotea! We flew Bari to Palermo in 50 minutes, inexpensive, reminded me of Southwest, 737 aircraft. They serve smaller cities. Good service at check in, no hassles. Visit Sicily from Puglia not Rome.
We spent 2.5 weeks in Sicily, our second trip there.
I am among the few who didn’t get excited by the Amalfi Coast.
Amalfi Coast, Capri, Naples, Sorrento: Stay on Capri at least four nights. Stay in the pedestrian path area between Punta Tragara and Giardini Agosto, sea views, no crowds.
I would definitly see Pompeii on this trip. It is between Naples and Sorrento on the commuter train line, Circumvesuviana.
Make sure you stay in Naples for a few days at least. Do not do Naples as a day trip!( especially from not from Rome.)
All of your time in Tuscany is planned in Florence? Take a week from Florence and rent a car, stay somewhere in Chianti region or Val d’Orcia. Or visit less crowded Umbria. Look at Spello.
We were in a Florence once in October and it was mobbed. However, one June is wasn’t crowded at all.
I prefer Northern Italy but it not a place “ to suck it up!” It is elegant and stunningly beautiful. we like it much much better than the Amalfi Coast and we are ocean lovers. We have been to Lake Como many times and the other lakes as well. We do not ever mix Northern and Southern Italy, one or the other works best for us.

The stay limit for non EU visitors is exactly 90 days (not 3 months), including day of arrival and day of departure.
If you want to visit so many locations you may want to have a different base every 7-10 days. When day trips are too long, it’s tiring otherwise.

You may want to follow the warm weather and move from north to south since you are visiting in the fall.

Have you been to Siena? There’s a lot to it - I don’t think a day trip would really do it justice.

I'm taking a similar trip in six weeks (!!!) and have a thread about it, just thought I'd share in case you want to see people's takes on my itinerary (which were very helpful). https://community.ricksteves.com/travel-forum/italy/three-months-in-italy

Malta is a wonderful visit for a few days. I flew from Catania for something like 54 or 58 Euros. Stayed in Valletta this past August. Lovely little city--And I do mean little. Easy to explore, good museums, very lively.

Do Naples and Pompei from Sorrento. Easy trips on the circumvesuvia trains. Naples has some nice sights but the city is a bit gritty for staying long term.

You could hit the east coast after leaving Rome or after Sorrento.

Neither Last Supper or Lake Como are essential. Depends on what you want. I have stayed in Verona and on Lake Garda nearby. That is also a very beautiful lake and wonderful city.

Thanks for all the help! Sorry Dave but I love to travel alone. That being said I am nervous about changing places, packing, transportation and hotels every few weeks for 3 months.

It sounds like I should just stick to the south and central and save the north for another trip. I definitely wrote down Volotea. I just hope it is still around in 3 years, I may reverse my plan around the south to start in Puglia then Sicily and up the coast. Once I have gotten to Naples I think getting to Tuscany for relaxing and being settled for a month will help. I was thinking if I rented a house for a month I could then go and spend a night or two in Siena and day trip to Assisi, Orvieto. Then the big city of Rome to explore until my days are up. Not one day longer than 90.

This would work flying R/T Rome. I've included Malta. If you skip Malta, spend these days in Rome on arrival. Traveling by air between destinations will save time on all these transfers but be sure to check individual airline luggage requirements.

Sept. Travel

Arrive Rome, travel to Florence. 21 days.

Week 1-2-3 Florence/Tuscany.
There are several Harvest festivals in Sept.

Sept. Fly Florence-Brindisi. 2H15m Alitalia.

Week 4 Puglia south. 7 days.

Oct. week 5. Puglia north. 6 days.

Oct. Fly Bari-Malta 1H 15m Air Malta.

Week 6, 3-5 days Malta.

Oct. Fly Malta-Palermo 1H58m Alitalia.

Week 7 & 8 Palermo-Catania. 13 days.

Oct. Fly Catania-Naples. 1H15m Volotea.

Nov. Week 9-10. Naples/Amalfi Coast 13 days.

Nov. train Naples-Rome.

Week 11-13. Rome. 21 days.

Average weather in Rome this month, lows 50s
Highs 70s.

Travel home.

This is just my weird brain working, hope it gives you some ideas.

Edit: 6 major location changes in 3 months.

Edit. I've not spent time in either Malta nor Sicily
So heed acravens advice below.

I would not start in Puglia or Sicily because of the weather. They could both still be quite hot in September. You can check actual, day-by-day, historical weather statistics for the last 10 years on timeanddate.com. I'd check at least the last 3 years; 5 would be better. Real day-by-day stats are better than monthly averages, and some of the averages floating around on the Internet cut off in 2000 or 2010. I think we all know weather has gotten more extreme since then.

Two weeks is my absolute minimum recommendation for Sicily. If you're going to depend on public transportation, I'd recommend closer to three weeks, and even with that much time you'll end up having to omit some worthwhile destinations. You probably will not go back there, because it's awkward to get to, right? So best to do a good job on it this time. I spent 17-18 days in Sicily in 2015 and do need to go back. Pick up Rick's new Sicily guidebook and read about all there is to see there, and note how scattered the sights are. It is definitely not a place you can visit by staying in one place. Depending on what you want to see, you'll need 3 to 6 bases there.

When I considered Malta in 2015 (but didn't go there), the ferry fare seemed crazy high for a comparatively short distance. I'd definitely look into flying. If you're going to have to fly, there may not be any advantage to traveling there from Sicily. Take a look at what other places have flights to and from Valletta.

It's a very long slog between Sicily and Puglia. A bus will be faster than the train (at least it was as of 2015) but still an all-day affair. I'd look into flying.

I use skyscanner.com to research intra-European flight schedules and fares.

I'm 68 and have spent the last 5 summers in Europe. All the trips except the first (3 months) were about 4-1/2 months. I try to avoid stays shorter than 4 nights, though that's not always practical. I often spend a week or even longer in a major city with a lot of sightseeing of interest to me, but except for London I've never stayed put over 10 days unless I was taking language lessons. I don't like taking a bunch of day-trips in the same direction because of the time on buses and trains (and the ticket cost, in some cases); I'd rather stay in a smaller place if I can identify 3 towns of interest in the same area. I find basing myself in a smaller place more relaxing than choosing only large, touristy cities. Changing hotels is definitely not my favorite thing, but in a smaller town the odds are good that I can find a hotel just a short walk from the bus or train station.

I use the bus or train time on my day-trips to relax a bit, and I am not an early starter in the morning. I build lists of sightseeing targets and try to allow enough time in each area to cover everything of significant interest to me, even though that limits the amount of geography I can cover. Perhaps that's why I don't get particularly tired on my long trips.

It has taken me 4-1/2 months to cover Spain fairly well, and 4-1/2 months in France has not allowed enough time for Paris and the immediate surroundings. (Both those countries required two trips because of the Schengen limit.) I wouldn't expect to cover the full length of Italy in 90 days, so I wouldn't feel bad about not getting to the lakes, the Dolomites, or any other specific place. Just choose areas that seem right to you--perhaps with an eye to the weather.

I would Start the trip in Naples/Amalfi coast while the weather is still good and everything is in full swing. See Pompeii from Naples. From there travel to Puglia. Maybe a stop in Matera for a night. Puglia is a wonderful area with amazing food. From there fly to Sicily and spend three weeks. Sicily is a large island with so much to see and eat. From Sicily fly to Florence then end your time in Rome, as it may be a little warmer than Florence in November.

So maybe 10/12 days Naples Amalfi coast area, 8/10 days Puglia, 20 days Sicily. That will leave you 40/50 days for Florence and Rome areas.