itinerary for 2 weeks in June

If you haven’t already booked the Athens to Santorini flight, I think I would fly immediately to Santorini after landing in Athens. That cuts the to and fro from the airport to downtown Athens to a minimum. If you do have a flight out at 6 am, you’ll need to take a taxi for about €65 from downtown Athens or sleep at an airport hotel. It’s about a 30-minute taxi ride to the airport.
From Santorini, you could go to the islands of Paros and Naxos in addition to, or in place of, Mykonos. Check out Paros and Naxos on YouTube as many find them a refreshing change in atmosphere from the thronged islands of Santorini and Mykonos, both of which have highly-trafficked cruise ports delivering tens of thousands of passengers to those islands during summer days.
Be sure you check Mykonos accommodation prices in June before committing to it.

When you depart Athens to fly home, you can take the 40-minute subway ride to the airport as the subway is open from 5:30am to half past mid-nite.
Have a great Trip!

According to a previous post you arrive at 8am on June 9th, and I agree with kenko, you could catch a flight the same day instead of spending a night in Athens.
Wasting a day by spending a short night in a hotel near the airport (or in Athens) and waking up the next day at 3 or 4 a.m. to catch your Volotea flight is pointless
On the day of your arrival there are 5 flights to Santorini between 10.30 am and 1.30 pm with Aegean or Sky Express.

I know that Santorini and Mykonos are the favorite islands for tourism marketing (and it's very effective!), but going to Mykonos is not going to bring you much in terms of authenticity. Just like in Santorini, you will join the first hordes of tourists of the year who are victims of this marketing, plus those who regularly come to Mykonos to party. You will spend at least 30% more euros than on other islands for equivalent services.

It's your choice. But as kenko suggested there are others.
Paros, Naxos and I would add Amorgos, the island of the movie "The Big Blue"
From Santorini to Amorgos there are Seajets fast ferries daily at noon for €75 per person, but there is also the Small Cyclades Line "Express Skopetilis" ferry which runs on Sunday 12th for €11 (departs 11.30am ).
There are many videos about Amorgos, here is one:

https://www.youtube.com/watch?v=zQqb89OzurA

So you could arrive in Santorini on the 9th and leave for Amorgos on the 12th.
If you stay 3 days in Amorgos, you will have another 3 before returning to Athens.
From Amorgos you can easily reach Naxos. There are daily connections with the Express Skopetilis or Blue Star or Seajets, or Paros with Seajets or Blue Star.

This version of the Islands part of your trip would be as follows:

June 9: Landing in Athens and flight Athens-Santorini
June 10: Santorini

June 11: Santorini

June 12: Santorini to Amorgos (port of Katapola) with the Express Skopetilis

June 13: Amorgos

June 14: Amorgos

June 15: Amorgos to Naxos or Paros

June 16 Naxos or Paros

June 17: Naxos or Paros

June 18: Naxos or Paros to Athens

June 20 about your trip Ioannina-Meteores (Kalambaka) I do not think you will find trains (maybe others forum members have more info), but there are buses in principle every day for Trikala

https://ktelioannina.gr/en/index.html

From trikala you can take a train to Kalambaka.

You don't want to do a hot and strenuous trip to sites in Athens after a long overnight flight. You need more than part of a day for Athens. I suggest 3 nights(at least one full day) in Athens at the end of your trip.

I agree with the others, just get to that first destination. My MIL really liked Rhodes.

I didn't realize you don't have any complete days in Athens.
I don't know if it's intentional.
Your program is already very busy, I would even say too busy, I don't see how you could add Athens

So, If you want to keep 2 days to visit Athens you will have to go back home later or make sacrifices :)

1/ By eliminating one of the 2 islands after Santorini and extending the stay on the remaining one by 1 day or 2, and return to Athens on June 17.

It has the advantage of packing and unpacking less often, wasting less time traveling, and better enjoying where you are.

2/ Or by keeping the islands and eliminating one of the visits on land

Would any of those have a party scene like Mykonos? That's what we're looking for in one!