How do we get to Crete without backtracking to Istanbul from Cappadocia? Feedback on plans?

Have you used something like Rome2rio web site to find your logistical options? I tend to use something like this for first layer travel planning. I go to the relevant website, however, to double check schedule and costs.

If by 3 days in Athens you mean 3 nights (which could be barely more than 2 full days, depending on the timing of the flight from Santorini), take a hard look at the transportation needed for the planned day-trips to Meteora and Delphi. As already mentioned, Rome2Rio is only a starting point. For accurate travel times, frequencies and fares you must visit the websites of the appropriate bus companies.

From Ephesus, Kusadasi has a ferry to Samos, Greece. From Samos, Greece there are flights to Heraklion, Crete (2-1/2 hours) via Athens or Rhodes.
Edited: I use skyscanner to lookup flights within Europe.

Ok so my sister talked to her Greek coworker who says to skip Meteora. He also says not to stay in Plaka, far too expensive. He also is from Crete so thinks we should stay a month LOL.

I’ll check out that website, thank u! I think we will stick to a plane to Greece. All those connections make me nervous:)

From the places you mention visiting in Crete sounds like you should be flying into Chania. Check out flights from Izmir. You will probably need to fly into Athens and change planes for Crete. Look at the websites for Aegean and Turkish airlines. The are both members of Star Alliance and excellent airlines.

There are lots of reasonably priced hotels in Plaka area - of course it depends on what you mean by reasonably priced....check out booking.com for possibilities and read the reviews, then go to the web sites of hotels that appeal. You can often get a better deal booking directly with hotel.

I agree not to stay in Plaka but not because of prices which can be lower than most, but because it is tourist central.
On Crete, stay in beautiful, historic Chania.

Cappadocia is served by two airports, Nevsehir (closer but with very limited flights) and Kayseri (farther away and with more flights). From either of these, you'd connect (most likely in Istanbul) to get a flight to Crete.

To find out who flies where from an airport, look at that airport's Wikipedia page. Remember that if a flight is "seasonal" the season can be long or short. Also remember that not all flights are daily; some are as infrequent as once a week.

To find actual flights, use Skyscanner, then book directly with the airline: https://www.skyscanner.com/
To find flights