You will definitely miss out on the best
This is just my personal opinion, but I feel it's important to mention it.
I believe all-inclusive mass tourism is ruining destinations. A rule of thumb for Crete is that the North (much more developed, with full tourism infrastructure) is much more touristy than the South. This is due to the remote and inaccessible areas in the South, as well as the mountainous and rugged relief in the South, compared to the North. You will find all kinds of all-inclusive hotels and travel deals for Crete, that's for sure. Many of those will seem attractive and will indeed be very very cheap. But traveling all-inclusive doesn't allow you to really get to know a place, go off-the-beaten-track, sit down and interact with the locals and create unforgettable travel experiences.
This is the best way to go about it, in my opinion: fly to one of the airports, rent a car and do as much exploration as possible. This will mean a lot of driving hours. But think of the endless stops you'll make. You'll be driving and stopping along the way on your own pace, in order to explore a cute little village you just stumbled upon, greet a friendly local, take quick photo of that beautiful eagle sitting on top of a tree, or just enjoy the sunset at the edge of the rock in silence. Also, this might sound a little risky, but it can definitely work out, especially during the shoulder months of the season: don't plan all your accommodation in advance. You might want to change plans along the way. Always choose small, family-run stays for the most traditional and local experience. Almost everywhere, there will definitely be a small guesthouse with a room available for you. At least this is what my experience has shown me so far!
Go check out my guide for the best free things to do as well as itineraries and travel tips to make your trip unforgettable.