1. Health bars. I'm so used to playing with them, it's very difficult for me to work out who is winning, when I should retreat etc. At least it would be helpful if there were some visual indication of which way a fight is going, such as bits falling off units (or something).
When you have a unit selected, the green ring under its feet serves as a "health bar". It gradually fades as the unit is damaged.
3. Building foundations could appear when placing a building. Friendly units should treat this area as an obstacle and try to navigate round it. If the building is placed in an invalid location, the order should be completely cancelled; the worker shouldn't walk over to the location and then idle.
Hmm... might be nice. Maybe some kind of translucent "phantom" building in its place would do the trick.
4. Gray out icons for units that can't be produced, and use a different font color for the resource(s) that are insufficient.
The "produce unit" button is already darkened out when you can't make that unit. I guess it might be nice to have an indication of what resources you're missing, but I think overall this isn't a problem worth noting (in my opinion).
5. Double clicking a building should select all buildings of that type. This already applies to units, I think it would be useful for buildings too.
I'm not sure where I stand on this one. It would certainly let you use Defense Towers more effectively, but I think the big advantage would be in production. Rather than selecting one Barracks and telling it to make four Guards and four Archers, and then selecting your second Barracks and telling it to do the same, you could kill two birds with one stone, so to speak. However, a
little bit of micro-management is okay in a game since it's another skill for a player to master. Personally, I think micro-management is the devil and I hate it, but other players say a game feels almost like it's on auto-pilot if there isn't any. As for myself, I agree with your idea, but I can't speak for whether the average player would want it or not.
6. Option to "loop" production. Just an idea, though I would never use it. 
I don't think I'd use it either, because I'd likely forget about it until my units started dropping dead of starvation.
9. Warning sound when under attack in another map location.
There is documentation for this in GAE, but I don't know if anyone's actually done it.
Perhaps buttons to center the camera on that location, cycle through each main building, and home in on the currently selected unit. Pressing a number key twice should home in on that group.
'b' cycles through buildings, if I remember correctly. 'spacebar' centers the camera on the current selection. This is in GAE, anyway. I don't play the others enough to know.
10. Should be able to command a worker to deposit resources by selecting worker and right-clicking main building.
Not a big deal, but I've had times when I wish I could do this.
11. Bigger group size limit.
Disagree! The unit size limit is part of the gameplay, and I think it's good the way it is. Glest is a small-scale skirmish game, and it is adapted well for that purpose.
12. Allow selecting a "default" attack for units with multiple attacks.
Do you mean defining it in the unit's XML, or selecting a unit in-game and telling it which attack to use (i.e. this Archmage will use Ice Nova and this other one will use Static Fire)? The latter can
kinda be done with a little XML modification of "hold position" commands, but it's not exactly pretty or ideal.
