This is a very impressive project. The higher resolution and new features are great, and the best thing is that most of the random crashing in the original RA has been fixed. I often play RA skirmishes with a custom mod (basically a heavily modified version of the old Future Wars mod) and the game is a lot more stable now in general. Thanks for all the work you've put into this. I noticed a couple of minor issues from what I'm used to in 2.00. I normally use this instead of 3.03, as the official 3.03 changed some things like AI allying.
I have a custom map with an extra base building AI, which works properly in 2.00 but not here. The "auto base building" trigger no longer does anything in skirmish. I can upload the map if it will help.
In capture the flag mode, everyone's flag is the player's color instead of their own color. CTF works fine in skirmish otherwise (and did in 2.00 as well, which had the right colors).
The AI might not always go to "easy" mode with the difficulty set to "hard." I have a lower cost setting for [Easy] in rules.ini so the AI will build more stuff, but the AI appeared to run out of money more easily in some situations. There may be nothing wrong here, but I seemed to see it frequently on one map.
There is a very minor bug in 2.00 where the darkness crate powerups can't be fully disabled, with Darkness=0 in rules.ini not doing anything. It might be already fixed here, but thought I would bring it up.
You had posted a screenshot of the AI building naval units earlier. Is there some way to enable this, or any of other things the AI never builds? It would be great if those could be turned on.