Some ideas for 3.3.8+. I don't expect most of these to be implemented overnight, but some are just simple tweaks.
1. Add the ability to choose player colors, or at least something in the network/custom game screen to indicate which team is which colour. Like displaying the player's nickname in their colour.
2. Steal GUI widgets, clickable resources and especially the guard and patrol commands from GAE.
3. Calculate data checksums on joining a game rather than when the game begins. Also, maybe do some sort of preloading for factions? Just an idea anyway.
4. Add the ability to save and record games.
5. Middle mouse button should reset the camera. Define a middle mouse click as a click without dragging (changing the camera orientation). This would free up spacebar for something more important like homing in on the current selection.
Pressing escape should cancel a connection attempt at the LAN screen.
Add shift+del and shift+a (or something) for deleting units and selecting all units respectively. Shift being required since these aren't commands you would want to perform accidentally. Deleting units being useful when units become trapped or so a nearly dead player can see the rest of the game unfold, and selecting all units being useful for that critical final assault.
6. Allow clicking inside unit bounding boxes, rather than having to click the unit itself, to make it easier to select units. In particular, I often have to explicit select the "harvest" command for workers rather than just clicking the trees because half the time I miss (and find them idling five minutes later).
7. Gray out button icons for units that can't be produced. On mouse hover, highlight the resource(s) that are insufficient.
8. When a group of units is given a command, ignore units currently morphing or producing a unit (summoners etc). Make it so that morphing units can only be commanded individually to avoid accidentally cancelling the morph command.
9. When a group of units is selected, show all commands, not just common commands (of course, only allowing units which can perform the commands to actually use them).
10. I'm not terribly keen on the two giant logos behind the menu buttons, one of them being just an upscaled version of the logo at the top. It looks messy imo. (But keep the GPL logo.)
11. Colourise the game info messages in the bottom left corner. Could colourise chat as well using team colours.
Perhaps add an option to display messages whenever a unit is built, a unit is attacked (until we get a warning sound for this), a technology is researched etc.
12. The default pointer is ugly, I usually switch to the system pointer at the start of a game. Which disappears incidentally when I press '/' at the menu screen and then start a game (until I press '/' again). Perhaps change the pointer to represent the command that will be performed by clicking.
For example, when a worker is selected, add a small wood icon beside the pointer when the pointer is hovering over trees.
13. When placing a building, a ghosted version of the building should appear at the target location until building starts. Allied units should navigate around it, enemies should disregard it.