I spent a few holidays in Crete orchid hunting in 25/04/95 -5/05 95 and found a photographed many species of mountain flora. I was based in Georgioupoli, near Rethymno which is really a bit too far from Heraklion.
I would suggest the Lasithi plain, some 60km south east of Heraklion From my notes we drove up to the top of the plain some 1500 metres in altitude. I noted, we found an orchid mine - four spotted, pauciflora, fusca, lutea, woodcock and others. also cyclamen creticum Spili and Gerikari were our favourite hunting areas and also the mountain Gingelos away over to the west at 2000 metres. There we had crocuses and anchusa caespitosa.
We had a fortnight to travel around and could have done with double that. Within reason, take the dirt roads and just stop and look for 15 minutes. Suddenly your eyes will pick out a flower and then they seem to appear in profusion.
If you stay away from the busy areas , it is likely that little will have changed.