I agree with Mentula that ProGUI gives a serious advantage over a player of the same level, if used well. However he didn't say what is in my opinion the biggest reason why this is the case (at my level that is).
The biggest advantage is in the case of continuous fights or harrassments, preferably in p1 or p2, where there are 3 or 4 production buildings per player. In that case, the attacking player can focus near all his actions in microing the fights, making threats, forcing his opponent to react accordingly, and he will still have near perfect production at home. Meanwhile, the other player forced to micro his fights as well will not be able to queue units at the right time and will fall behind because of it. The population deficit will grow until the game is definitely over.
I think that it is quite a big advantage. For comparison if used correctly by a good player it would be kind of as if a player is with a game speed of 0.7 while his opponent is at 1.0, normal speed. While both players have the same skills and would make a good decision at a good time, having your game slow down allows you to make more actions that are valuable at a critical time of the game. However, if both players are booming, it makes almost no difference as both players will have the time to do all meaningful actions, and the boom will be the same. It may still boost some players' booming ability, so it may also be unfair for that reason, but i don't really know about that personally.
I am saying this based on (maybe a bit limited) experience. There's a certain player that has a similar skill level as me. If I recall correctly I have a slightly higher win ratio against him when he is not using ProGUI. However when he used ProGUI I had 0-3, and it was not even close. He simply made what I think is a perfect use of the mod, forcing fights mid-game and getting a pop advantage I could not recover from.
I will give a little more intuition on how this can affect competitive games by giving the example on how macros are viewed in Age of Empires 2. Basically, any kind of macro is banned, and you can see in this video how even the simplest macros are problematic:
0 A.D. is not AoE2 of course but still that shows macros can escalate into a huge advantage. So if powerful macros are found with @Mentula's mod then that gives what i think could be an unfair competitive advantage as well.
The same can be said with autociv where building hotkeys give a huge advantage (when used properly, of course). The difference for me is that it is a feature that should so obviously be in the game, that it makes it fine. But anything further than that, I am not so sure. AoE2 also had some grey areas with the building range indicator, and some mods like small trees or age of cubes.
I hope you see my point. I personally wouldn't mind too much in team games which are less serious and where we try to balance it before game start, however if I expect the game to be competitive when I really want my level to clash with the opponent, that's gonna be a problem for me. Of course I know that neither @Atrik and @Mentula intend to do any wrong and I respect the openness of your programs, but still that can cause a problem when a powerful feature is released.
Personally I would like very much for the AI to have an enhanced training algorithm. Personally a long time ago I modified their queuing algorithm to grow population faster, however it is not worth much as I didn't touch the other parts of the AI to go with it. We can see that in the following screenshot where my AI (red) grew population much faster in the early game than Petra (green), where they both had the same gather rate at a medium difficulty each: