Just some gameplay ideas since we're getting towards a stable release...
1. 3D positional sounds.
2. Revamp armour. The current armour values aren't really very interesting... stone is stronger than wood in all situations but one (and equally strong in that case), Organic and Leather are weaker in most situations. Might as well adjust unit hitpoints a bit, then come up with some more interesting values.
Also, maybe rethink the attack types a little. Is the Arrow type even used?
3. Workers should start work on buildings from the nearest side. A placed building should have some sort of marker (ghosted building, building foundations). It should be possible to command additional workers to work on a building by right-clicking on this marker. When a group of workers is instructed to build, they should all work on building. Friendly units should avoid building markers (treat them as areas they shouldn't walk through), while enemies ignore them. Also, maybe allow placing a building on top of allied units, which could move aside when building starts.
4. Map previews in custom game screen.
5. Allow selecting more than 16 units simultaneously. If you're able to create that many units, you should be able to control them.
6. A fixed unit cap to discourage turtling in multiplayer, and reduce inevitable lag/slowdown. Most games have some sort of cap...
7. Allow commanding units by right-clicking on the minimap.
8. The Indian faction has the position of housing and gold reversed in the resource indicator at the top of the screen. (Well, all the other factions have it the other way round).
9. Separate options for "no fog" (map fully visible from the start) and "reveal map" (map fully explored from the start) in the custom game screen. I had a bash at this, but didn't quite get it to work.
10. Hotkeys for all unit commands (based on the position of the command icons on the screen).
11. Allow commanding workers to dump resources by right-clicking on a store building.
12. A masterserver that can actually host games. Eventually
13. Remove dead units from the minimap immediately.
14. Units generally shouldn't be able to hurt themselves with their own attacks. Maybe there could be an option to turn off team damage too.