I'll echo the complaints about the fly spell.
Fundamentally, that spell is just too good. It is Superman/Peter Pan level flight, as a fairly low level spell, and can be cast on anything. It completely changes the game in strange ways. All of those are big problems.
Also, the fly spell works to seriously negate some cool things in campaigns, namely flying mounts or other cool flying gadgets. Why try to tame a pegasus or griffon in D&D when you can just cast a fly spell on the party fighter instead? Why get a flying carpet when you can cast Overland Flight instead?
I would be happier if they got rid of the Fly spell completely, and kept flight in the hands of special creatures and magic items, but barring that, some of the suggestions made here about enchanting items temporarily and lowering maneuverability sound good.