First timers in Greece!

Your plan can be done however you are looking at a number of hops that will take up at least a total of one full day of your 2 weeks.
Your plan to fly to Milos for 3 days. Fly back to Athens and connect a flight to Crete. Fly from Crete to Athens and connect to a flight to Naxos. Fly Naxos to Athens before your return flight.

You are going to be spending a lot of time waiting around airports.

If it were me I would fly direct to Chania on day of arrival in Athens. You need a minimum of 2 hours to make a connection. In September it is still at the early end of the high season so maybe 3 hours for the connection.

You are going to love Chania particularly if you can find a hotel inside the city walls. The old town and waterfront promanade are beautiful.
My advice would be spend 7 nights in Chania. There are lots of day trips in the area that can be done by excursions or the local KTEL bus goes pretty much anywhere you may want to go for day trips. Consider taking the bus to Kissamos where you can hop a ferry that takes you to Gramvossa where there is a lovely beach, a shipwreck and a pirate fortress. The excursion then takes you to Balos Lagoon which is a huge beach area.

I can recommend Wanderlust tours which can take you to the best locations in West Crete. Max 12 people. Since we stopped driving we have taken 4 of their tours.

Your week will fly by in west Crete.

Fly back to Athens and connect to a flight to Naxos. As far as I can see, there is no direct flight from Chania to Naxos so you have to connect in Athens. You can be in Naxos by noon.
In Naxos I would suggest you look for a hotel at St George beach. Its a lovely sand beach and is really part of Naxos town just a 10 minute stroll around the headland to Naxos waterfront promenade. Naxos has other excellent beaches along the west coast with newer resort hotels built in the last decade.

Greece is a destination best experienced slowly. Thus I am suggesting you drop Milos. Dropping that hop is going to give you about a full day of extra time on Naxos or Chania.

Your plan to spend the last 2 days in Athens is good. You always want to be in Athens the day before your return flight. We were on a delayed aircraft Naxos to Athyens and half the passangers missed their return home flights.

For fun here are some images of Chania and Naxos
Wanderlust tours Chania https://www.flickr.com/photos/stanbr54/albums/72177720318394812
Chania 2024 https://www.flickr.com/photos/stanbr54/albums/72177720318408008/
Trip around Naxos https://www.flickr.com/photos/stanbr54/albums/72157634605629689
Naxos 2025 https://www.flickr.com/photos/stanbr54/albums/72177720329571437/

We are looking for a somewhat slow-paced and relaxing vacation.

We would love to do some hiking.

We are planning on renting a car if necessary and definitely want to
explore villages.

Considering the time you have available, everything you've said about what you want to do and how you want to spend your vacation in Greece, you should skip one island.

How do you plan to explore villages, go hiking, and relax if you only stay, for example, 3 days on Milos? Within those 3 days, there will be two half-days of flights and transfers. So that will basically leave you with only two full days.

The same goes for Naxos, which is the largest island in the Cyclades.
Not to mention Crete, which requires at least 15 days to explore even part of it.

Are you sure you can't travel by ferry? From Heraklion to Naxos, while there are flights in September, they're only three times a week. Having to fly to Athens to cover the barely 100 miles between Milos and Crete is quite a detour.

All these trips will take up a lot of your time, time that will be anything but slow and relaxing.

Definitely start in Crete and focus on the western part of the island if you’re interested in hiking and beaches.

Have a look into the southwest coast as it offers a great mix of trails, seaside villages, beaches and coves. These trails are leading along (E4 long distance trail) beaches and coves or even have them as destinations (Samaria and Aradhena gorges). Some trails can be demanding though, so do your research.

Another lovely combination of (easier) trails and villages -plus great food- are the rolling hills of Apokoronas region east of Chania.

Also, Balos Lagoon can be reached over land. There are several companies offering off-road tours (don’t attempt this drive in a rental car), followed by a bit of a strenuous short hike to the lagoon.

My suggestion would be to fly into Chania first and out of Heraklion if you want to spend time in Naxos as well. I’m afraid you’ll have to drop Milos considering the time you have.

Last night in Athens: don’t bother staying close to the airport. No fun and expensive. In Athens there are numerous hotels offering shuttle services to the airport any time of the day. Depending on departure time you can also consider staying close to Monastiraki metro stop (Psyrri, Monastiraki or Plaka area), where the blue line takes you directly to the airport.

I must respectfully disagree with some of the comments you have received. I have been coming to Greece every couple years since 1970.

1. The fact that you are coming from the US west coast....makes a long journey to Greece. We come from Seattle and the last thing we want to do when we land in Athens is get on another flight ( even short) and travel yet some more. We always stay in Athens the first three nights, explore the city, do the sights and then head out to Crete....jet lag over and ready to explore.

2. I don't agree that it takes 2 weeks to see Crete. You don't have to do it all in this first trip. A week is a nice chunk of time to visit and get a feel for this incredible island. That said, I don't know why Western Crete has become everyone's focus, making it over touristy and crowded. ( I would never go to Chania again ... it was the one town I felt claustrophobic and overwhelmed by the amount of tourists.) Have a look at Eastern Crete. Less tourists, beautiful vistas, wonderful hotels and restaurants. Look at Aghios Nikolaos as a base.

3. We always do the Athens Sofitel our last night in Greece before going home. Flight connections to the West Coast of the US usually leave very early morning and although it is expensive we splurge and stay at the Sofitel for the night before our departure. To get up early morning and walk 100 meters to the check-in counter from the hotel.... is worth every drachma for us.

2 days in Athens!!!?? Aren't you planning to see the Acropolis and amazing Parthenon?

You can also go with this itinerary like:

Day 1: Land Athens → Fly to Milos
Days 2–4: Milos
Day 5: Fly Milos → Athens → Crete
Days 6–10: Crete (choose one region)
Day 11: Fly Crete → Naxos (or via Athens)
Days 12–15: Naxos
Day 16: Fly Naxos → Athens → Overnight → Flight home

or for your girlfriend’s 40th, i would recommend a special dinner in Naxos or Milos. Both of these islands have excellent seaside views where you can celebrate in a relaxed, authentic setting. or if you need more information don't forget to check vacationotrips before travelling.

If you do omit Milos, and if you fly to Crete first, I suggest checking to see if there are direct flights (all on one ticket) from San Diego to Heraklion, Crete. This way you don't have to worry about how much time you need in Athens to get your luggage and then get to your next flight. And if you do miss a connection, the airline is responsible for putting you on the next available flight, as long as all of your flights are on one ticket.

We have friends who fly to Crete every year from Boston. They never go through Athens. They fly on one ticket, usually with a stopover in Zurich.

When we traveled to Greece several years ago, we flew direct from Boston to Santorini (our first stop) with a layover in Zurich. We didn't have to worry about our luggage until we landed in Santorini. It was so easy.

Most of the ferries you would be taking are large and very stable on the water even in rough conditions. I've taken them a few times and never got sick let alone experience a rough ride.

If you are flying from San Diego on one ticket that means two stops before you get to your final destination and everything involved with flying.

Could be a long day/flight time if that is an option rather than staying in or near Athens before going to a final destination.

Then there are the other flights for island hopping. Lots of flying/airport time.

Would just one island appeal to you to avoid the extra traveling? Crete is the largest Greek Island and would take weeks to fully explore.

Naxos is the largest of the Cyclades Island and there is more than enough to do there for your time.

If Athens doesn't appeal to you upon arrival you could go to Rafina, a small and rather nice town. It has a port for several of the Cyclades. The Avra Hotel has free transfer service from/to the airport.

Maybe the best option is to fly direct to Athens on one ticket then purchase one from either, Aegean or Sky Express for the next available flight to an island. It has been done by hundreds of people and if there is two hours between flights you'll be OK.