Heraklion
The only good things I can say about this city is the cheap food, and some cool bars in city centre. That's it. I know, I saw the city only a few hours, but what I saw was just chaos. No urban plan, it's just a mess of bad roads and a mix of modern buildings in between ruins of old buildings. This city it also introduced me to how cretan drive, which is bad, really really bad. It's essentially the far west of driving. To get to the airport to get the car I rent, we went to the Bus station, we got the ticket, and then they told us that the bus for the airport doesn't leave from there, but we had to walk half km on a not very safe road with insane sidewalks, and then get the bus there. 
Why one of the main bus lines, that supposedly should serve to all the tourist coming to this city, is hidden in an industrial area, it's mystery, and a non-sense.

Rethymno
This city is on the way from Heraklion to Chania, it's a nice little city with a nice old town and a decent beach. It's full of small and medium restaurants, and it's definitely better than Heraklion, but it shares the absolute lack of any urban plan, and to be fair I still have to see a city with an urban plan with a minimum of logic.
We spent the rest of the morning and the early afternoon in a nice beach, well organised and with reasonable prices.
Unfortunately after that we got caught by one of the worst restaurant in the city, maybe in Crete, possibly in the entire universe: Mouragio Maria.
The food is ok, but the waiters were extremely pushy, as they invite us to see the restaurant and after a second we were seated on a table. They don't give you time to watch the menu, prices are unclear, and they always push you to take the most expensive dishes. At the end we spent 67 euro, which is an insane amount of money for a meal in Crete, for very oily and greasy food. If you go to Rethymno, don't go to this restaurant.

Chania
After the very expensive meal in Rethymno, with a big pain in the butt, we headed to our hotel in Chania.
The hotel was nice from the outside, it has an incredible view of the entire city, a beautiful swimming pool, and the room was clean and nice enough, the only downside of this place was the bathroom, which has been a big pain in the arse as both the handles for the shower and the sink were nearly usable.
The city is again a mess, and you can clearly see it from the hotel view, but the city centre, with its small streets full of good restaurant and shops it's very nice, so far the nicest city in Crete. If you can find a parking and if you have a good GPS, as to drive in the streets of this city is quite confusing, you definitely have to visit this city.
We went to Tamam, a really nice and really busy restaurant in one of the many small streets, and for less than 30 euro we ate an amout of food for 4 people (we still have to figure out how much food to order here), and the quality of it was excellent.

Note if you are going to rent a car: if you are not a good driver, this island is not for you, unless you will to pay plenty of money to your car rental. It's a jungle, cretan drivers will try to surpass you at any time in any direction. Parkings exist, but it's for pussies, real men here park everywhere, and when I mean everywhere I mean everywhere. This place is only for tough drivers.