The lack of loot/items from defeated heroes. Could be just one item at random. AND if my sov/hero has a "pickpocket" skill, I get to choose which item I steal.
The lack of positive/negative fame for winning/losing battles/cities/outposts. If I win a surprise victory against a superior force, i should get a boost in fame.
Fame/infamy could also be used in a GalCiv type alignment system. The "quest" screen where the cruel dog killing men come to see you and you have three choices could reflect this. Different heroes could desert you if you become too good or evil.
The lack of consistency in spell effects, certain spells can only be cast once, etc. (Look at Demons and Wizards mod for a solution to summoning.)
You briefly had spells that were hybrids of two schools, these were great.
Spell books should be big boss or wildland quest rewards, not for sale in a Pariden shop.
All spell schools should have a damage type and it should be consistent with weapon effects/resistances. Totally agree with going with a Diablo-type of prefix\suffix item crafting randomizer.
Creatures and interactions with items/spells should be consistent. The Holy Hammer did not kill Banshees last time I played for example. And one of the Venomous bows doesn't do poison damage every turn.
Tactical battles/city building/boring unit traits have already been covered by others above.
Weird/shifting outpost/city ZOC that makes me waste time rebuilding structures in my precious city queue.
Bribe\hire modders to incorporate their mods into the vanilla game. Hold forum contests for new quests/monsters/items/heroes etc.
Why do I have to go to a third-party site to get mods?!? Where is the Hosten's Library on the FE:LH site?
Where is a mod manager, monster/creature editor, loot editor, etc.
Thanks for creating this thread... I feel much better.