Hello and congrats!
There is no right or wrong way to do this and everyone travels differently.Personaly I think you may want to get a flight first thing to the islands upon arriving in Athens airport so you do not back track and been able to delag on a more relaxing setting. I would not want to explore archeological sites or walk on a city dazed after a long trip or even worse drive. Furthermore getting to know a bit the local culture and the history/sites of other locations would make an Athens visit easier (knowing where all those exhibits on National Archeological Museum come from, understanding a bit where locals' behavior comes from and been accustomised on ways things are done, this kind of thing...)
I find Santorini very very touristy and artificial and Oia even more so (unless you believe your averrage local still live in cave houses, moving around on donkeys and/or have an infinity pool on his house), but I understand its appeal too and I believe that as far as you make an effort to go there, you should spend at the very least 4 nights/3 full days as there is lots to see and do even on this tiny island. I never get why people make all the effort and spend money to go somewhere and then spend only a few hours or a couple of days.
On Crete you need to pick only a specific area or plan carefully how travel logistics work and cherry pick a couple of places rather than trying to see it all. It is a huge and very diverse island. Connection port to Santorini is Heraklion.
I think people tend to stereotype for Athens. I do not think many people would go to Paris or London only for 2 days, so why to do this on Athens? I find negative comments about Athens coming mostly from people with wrong expectations and limited planning. Athens is crowded (yes, really, a 6 million metropolis crowded, can you believe it?), not much to do other than visit the archeological sites (really? what would you like to see and do that it isn't there?Volcano climbing maybe not, not so common on most capital cities globally I would think?), dirty (where did you see rubbish on the streets on Athens? You could eat your food out of metro stations floors for heaven's shake!) and so on. Depending on what you want to see and do there you could spend weeks and I think in order to get a decent understanding of the major archeological sites you should do research and take it easy and plan avoiding the busiest and crowdiest parts of the day. And definatley visit two or three related museums to get a better understanding on what this is all about. So at least 2-3 FULL days are necessary only for this.
I think it is a pitty so many people skip mainland in favor of the islands. Mainland offers a much more diverse experience than most islands and does not lack of things like beaches and the like either. On my opinion people have a wrong approach though. While they say, "lets go to Santorini for 4 days" and they tend to be based on one spot and are keen to explore around, on mainland they never say "lets go to Delphi for 4 days" and explore around, they say "let's go to Delphi and Meteora and Mt Olympus and Thessaloniki and here and there and furtheraway, covering major distances popping from site after site without really exploring each area. I understand that some balance has to be made here, most people want to check more than one spot, but this doesn't mean that they have to run around all the time. Moving say 20 kms from a popular place on mainland you may find many interesting sites, sights and activities and have a better chance to experience local life too.
Of course it always come down to personal preferences and specifics, but those are just my views.
You need to be aware that a car comes handy to explore the mainland and that hiring from one spot and dropping on another is not always possible and might involve high drop off fees. Usually doing a loop starting and finishing at the same place works better.
