No, AI is divided into several parts. Some of them work with 3D, although in case of Heroes the impact is small. 3D is not only flying, there's objects interaction, running uphill, downhill - calculating terrain movement cost, calculating path on the battlefield for flyiers. (If there's not and won't be Fly Spell.)
For other games, you often can use "Fly" Spell or you can just "Fly", for examle in case of MoM you could use "Flying Fortress" to lift up your Fortress and prevent attack from any landline rats. 3D aspects are presented in 2D games, that's normal.
I wasn't playing the game, judging only from videos and available information. But there's seen a lot. For example world map was simplifed, which make it better. And that's not the only thing which was nerfed.
As for long loading times, that's bad and I expect/hope that they will fix that.