another UI: Could we please have a way to sort our designed units, especially in the Train menu? According to labor, material, crystal, weapon type would be nice, or also custom drag-and-drop. Default is currently unchangeable, and that is by design time.
AI cheating: It would be nice if the AI would get more cheats which benefit it later (I am only challenged until the end of Early Game, when I can be steamrolled by AI), such as increased research bonuses per turn (e.g. hard faction gains +1 research every 10 turns, expert +1 every 5, etc.).
Population mechanic: It would be nice if there were some incentive to growth/population past reaching level 5, such as a marginal bonus to gildar, research, and/or production.
For the love of God, please consider having non-hostile entities (units and structures) be able to move through / stack with each other, the current pathing computations can occasionally cause game-breaking logistical nightmares.