It's not about numbers, it's about some players being better than other players. I've played enough centers and this community is small enough (I play exclusively 6s) to the point where I know every player that frequents centers and I've been in the competitive scene long enough to know all the players that also play ESEA/CEVO.
Having an ELO system based on hours/centers played would be bad for the reason you stated. But I don't see the relevance of that because we're talking about scrambling teams randomly.
Any fair PUG system has either captains or a team scramble. Does that mean every single pug will be close and none will be rolls? No. So why do they implement it? Because it helps.
Let me address both of your concerns:
1.) This won't stop all stomps.
A: You're correct. However, the very nature of something being random (and the option to scramble again after teams are set) makes it more likely to be balanced than it currently is.
2.) But I want to play with my friends.
A: You're free to do so. This is probably the most selfish reasoning behind being against this suggestion, however. This is equivalent to thinking that 6s shouldn't be included as a game mode because you'd rather play highlander. The world doesn't revolve around you or your friends, and there's plenty of centers and the ability to rent servers to create your own.