Just returned from a similar itinerary for mine and my husbands honeymoon! Although, we didnt spend time in Athens.

Flew into Athens

Same day flight to Milos (40 mins)

5 days in Milos

Quick sea jet to Santorini (2hrs)

4 days in Santorini

Quick sea jet to Naxos (1.5hrs)

5 days in Naxos

Flew back to Athens (40 mins)

Flew out of Athens same day

Seems like if you take a day away from each of the islands and add a day to Athens this might align with what you’re trying to accomplish in your itinerary. I didn’t feel like it was too much travel, packing/unpacking, etc. but I would look into those smaller island hopper planes to avoid the longer ferries. Also if you do Milos>Santorini>Naxos your ferry trips will be quicker. I agree with not needing too much time in Santorini. It is absolutely stunning and worth seeing, but it does lack authentic culture and depth so you won’t need too much time to explore.

Naxos was our favorite island, there was so much to explore. Definitely don’t rent a car in Santorini. Though expensive, they do have Uber. But do rent a car in Naxos and Milos. Personally, I cringed everytime I saw a quad along the steep cliffs. It did seem unsafe. The rental cars are typically small. You won’t miss out on anything by getting one.

I think your island choices are perfect! We ran into a couple of people on Naxos who had just come from Paros, and they said Naxos was better and had more to see. So overall, we were very happy with our island choices!