The unit "balancing" makes countering enemy attacks insanely difficult and the pace of the game is just way too fast, it doesn't feel like there's any "strategy" - just constant countering and trying to wipe your enemy out before they counter the units you tried to produce that they don't (currently) have anything capable of stopping.
I first noticed this sort of "balancing" in AoE2 (before that I was playing C&C/RA, Starcraft and Warcraft II), it was just as annoying then as it is now, for the exact reason you wrote. I think this is an extremely lazy way of balancing the units and factions, especially when it feels so artificial and arbitrary (in RA3, for example).
The way Blizzard balances the units/factions in Starcraft is far superior. It is an entirely different paradigm really, because in it you are never punished for using the "wrong" units, instead you are strongly encouraged to use combined arms and take advantage of the strengths of each type of unit so as to minimize your loss, or in other words, to make your investment more effective. For example, if you want to take down a siege tank with marines, you can. You will suffer some losses but you can do it. However, if you use a ghost to lock down the tank first then you won't suffer *any* loss. This is how you create an innovative, fun and rewarding gameplay in an RTS title.
Now compare this to C&C3/RA3. Ever try to take on a single APC with your infantries? They get mowed down so fast it really doesn't matter how many units you send in. So you are forced to call in heavy armor, where the aforementioned APC will suffer the same fate. Is it balanced? In a way, yes. Is it as fun? No.
This is not to say you can't create an excellent RTS built upon the rock-scissors-paper model -- Company of Heroes immediately comes to mind. I guess there are just a lot of factors in a game that need to be carefully thought out, and frankly EA's track record doesn't inspire much confidence as far as the upcoming expansion is concerned.
At least Starcraft 2 is coming.