Turkiye to Athens Greek Islands Itinerary puzzle

In October, there are indeed daily ferries from Kusadasi to Samos, 3 times a week from Samos to Mykonos (a 5-6 hour ferry ride), daily ferries from Mykonos to Naxos and from Naxos to Piraeus.

But could you explain why you chose these islands and why you only want to make brief stops on 3 islands and not visit them?
I don't see the point, given that you only have 9 days, and you need at least 3 full days to briefly visit an island and almost a whole day to get from one island to another.

I was really hoping to ferry rather than fly, seemed like a more interesting way to go. I want to know whether there is a good, scenic, interesting path to travel from Turkey to Athens this way, if I'm missing a better path. Happy to research other suggestions! I chose the islands based on reading guidebooks and itineraries, fall ferry availability, and access from two potential Turkish ferry ports.

Looking at Ferry hopper, it appears we could arrive Samos mid morning, have 3 days in Samos, just one full day in Mykonos (just exploring what we could by foot, but it is a necessary midway point to get to Naxos or another island within easy distance of Athens), then most of 4 days in Naxos. So really 2 islands in 8 days, with the midpoint quick stop for ferrying purposes. It is a long 6 hour ferry between Samos and Mykonos, yes, and a long night ferry from Naxos to Athens. I view that as needed down time!

Similarly, if we began in Rhodes, we'd have 3 days in Rhodes, a short 2 days in Kos in order to ferry to Cycledes, an overnight ferry with a sleeper cabin to Naxos, and nearly 4 days in Naxos.

If there is a better suggestion (I'm anticipating I'll get some "don't bother, just pick one island and fly") it will help guide my further research and be ready when ferry schedules launch in the spring. If just one accessible from Turkey, which? If just two that can be accomplished by ferry, which?

Ferryhopper is convenient, but it won't give you the October 2026 ferry schedules until August 2026.

There are very few ferries that go from one island group to another, but these are subsidized routes that operate 365 days a year, and their schedules hardly change from year to year.

Besides the Samos-Mykonos route you're considering with the Blue Star Mykonos before continuing on to Naxos, and since you mentioned Rhodes, you could also, instead of going from Rhodes to Kos, take the Blue Star Chios Rhodes-Santorini (3 times a week) and from Santorini a ferry to Naxos (less than 2 hours by ferry).

Then, the Naxos-Piraeus ferry takes about 3 hours with a Seajets caramaran.

I'm not a fan of either Santorini or Mykonos, but if I had to choose between the two, I'd take Santorini.