Chapter #1
First things first -- staying in Iraklion. I like Hotel Kronos if you can get a balcony w a sea view... it's right on the sea front, and walkable to the bus station. Reasonable rates. You can get a rental car delivered right there .. but DO get good directions for getting out of town! Iraklion has 1-way streets, very confusing... once u are on the highway heading west, no problem. When you return to Iraklion to get the daily 9:45 ferry to Santorini, u can arrange just to leave y our car in a certain lot by the ferry.
Now, about this "Base" fantasy. People who talk about having one "base" in Greece usually got the idea from visiting Northern Italy. Rent a place in Tuscany or Umbria, and every day drive 20 minutes in a different direction & have a new experience, N - S- E -W in 4 days, then back to "base" in half an hour & sleep in same bed.
Greece is not Italy. In small islands of course, if you go 20 miles in ANY direction you drown. So you spend 4 days in one island and hop to another. That's why they call it island-hopping, not island basing.
Crete is as big as a country, but also has its limitations as a "base" concept. Because of the major mountain ranges, you cannot go any direction you wish ... only down the valleys between mountain ranges. Thus you spend a lot of time getting there i.e., Chania to Paleochora and then you have to backtrack. You spend all your time in the car. this online map which I love (click & it gets huuuge) http://www.explorecrete.com/crete-maps/images/Crete-eot.png - has roads AND terrain & shows plainly what I mean.
Certainly CHANIA itself is rewarding for 2-3 days to explore.. and you want to stay on the WEST side of Old Town near the wall -- the main "lane" (no-cars) is Theotokopoulos street, and it is absolutely LINED with small pensions that have what you call "studio units" w. small kitchenette or kitchen "ell" w sink/hotplate. ALL rooms have FRIDGES most also coffeemakers, small table & chairs. Just a few of the places along that street include Hotel Hera & Casa di Pietra (the 2 with the BEST location.. at end of street nearest the sea), then either on Theo or just off include Anemones Apts, Pension Nora, Iason Studios. Casa Veneta This terrific map https://www.hotelscombined.com/Place/Chania_1.htm?mapState=expanded%3D1 shows this cluster of small lodgings (6 -10 rooms) u are planning so far ahead no need to using an online agency, just look google their websites, look at their Trip Adv reviews, then contact 5-6 of them direct ... they'll be delighted because that means they don't have to pay an agency fee. This is hands-down the best area to stay in... there is free parking at a lot right by the seafront (look carefully, one lot also charges), then you roll your little bags up a gently ramped walkway to the foot of Theo. street, and there you are!!
Sure, enjoyable day trips: Akrotiri Peninsula , the ancient ruins of Aptera, Rethymnon, (mainly for the Fortezza its Old Town isn't up to Chania's). To see small villages enroute to Rethmymnon, jump off E-W Highway (on the map, Big Green Road marked E75) drive instead Old Road, in Red ... on this, one May we ran into "traffic jams" of herds of Goats & sheep meandering along. FOr more villages, head for VAMOS (see map)up a road near the sea, to Gavalohori, a very traditional town w. crafts. Then swim at a beach like Almirida or Khalives, & return to Chania. On yr drive West, detour inland at Panormos 5 - 8 Miles to Cave of Melidoni ... gorgeous stalactites, yet haunted -- in 1823 Turks suffocated over 300 civilians there ... a simple pile of stones erected at the time says "never Forget" ; poignant, unforgettable.
However -- that's maybe 4-5 days, u have 10 ... time to Move Along! I've reached the word limit... so will continue in Chapter #2.