CoH is not big enough to split the community any further, we cannot separate randoms from arranged teams and let them play on different ladders.
Yes we can and nothing serious is going to happen. The people that love COH2 will keep playing with AT against other AT. The only people that will "suffer" from it are the idiotic noob stompers that only expect to win on good coordination and massive blobbing. The thing is that's viable in COH2 to this day, that's why people do it. Put em separately, nobody will give half a shit I promise.
And my experience mostly comes from 2v2 and 3v3 with 2 similarly skilled friends, which makes it way easier for the match maker to find opponents [...]
So you talk about a problem in which you actively take part or at the very least take advantage of.
There is no feasible way for CoH to create even more separately handled ladders without killing the game outright. The only option is to somehow get 5x or so the player base on a constant basis, and that's not going to happen.
That's fear mongering. Of course some people are goin to be unhappy, but the overall majority will be happy. You cannot just dismiss all the criticism with a simple "but the game will be worse".