I am a long time player of Shadow magic.
I know it may seem trivial, but I liked the option to name cities that I start. I suppose its an RP thing, but when I have a dwarf leader with a scar down his face named Tyrian Lannister and I start a city, I would like to name it King’s Landing.
Less trivially, There were generally lots more overland spells to cast in Shadow magic. Sometimes in AOW3 I get stuck with literally nothing to cast while mana accumulates. Having a resource accumulate is one of the main signs of a noobie player, and here I watch it happen to myself quite frequently. I don’t know what the arguments were against unit enhancing spells, maybe they were good arguments, but I sure miss mana being the limiting factor in the spells I cast instead of just “well, nothing useful to cast this round either. Oh look, 600 mana and climbing.”
The flyer combat thing upset me when I first heard about it, but its ok now. Its just different, as was pointed out in another thread.