I'd be inclined to think that the chief reason for the centralisation around the CAPs would be, as I stated on IRC, the fact that almost every CAP made was designed to not be threatened by the top Pokemon in OU, and the common battle conditions prevalent - the last 3 CAPs (counting Voodoom) have all been resistant to Stealth Rock, and all have some means of forcing down the most popular Pokemon in the tier (see: Scizor, Heatran). Hence, the CAP Pokemon have created a metagame where all the old standards are either a) not as effective due to type considerations or b) thoroughly outclassed. Being not-so-effective, they fall in usage, and the void is replaced by those that shoulder this new metagame - those that we specifically designed to be the best of their kind in ANY metagame. To this end, we gave them incredible abilities, bloated movepools, useful stat spreads and a specific niche in the metagame - hard to shift, rather like a more balanced Heatran effect. Just like Doug said:
They've been good for a helluva long time -- yet there always used to be room for a lot of OU standards too.
Yet there isn't now. There are so many of them that they've created a metagame all to themselves. We created these Pokemon, whether consciously or no, to be top-tier, and now they are at the expense of the old standards. Without radically changing the way the process works I can't see any solution for this - All TL's supposedly want 'their' project to be a success, the community wants a new, exciting, powerful presence - short of draconian new rules.
And this adds another bit of trouble too - the reason CAPs are so good is that we intentionally give them an unexplored niche, which they then perform better than anything else in the game. If we take this part out, we're getting rid of the learning experience, which is in my opinion the single most important part of the project, and we are reducing ourselves to creating something 'imperfect' - much less reliable and therefore not guaranteed to help us learn anything.
This seems to be a theme that can only get worse, and highlights something I've been wondering for a long time - what happens when we have 20, or 30, or 50 Fakemon running around? Nobody can really believe that then, there would be a metagame even remotely recognisable to the one we have now. If this is a problem, I see no solution, short of putting them on a sort of rotation or only bringing out some for special events, like CAP Tournaments. I guess I don't have anything to say on this point, but I think it is something that the Policy Review Committee should consider when the PR thread rolls around.
I don't have anything to add that hasn't been said already (RE. Rey's 'mini-metagame') so I guess I'll just stop here. Of course the cynic in me says that this could simply be a case of "You don't come to a CAP server to not play CAP" - but I would have to agree that if something can be done to break up the centralisation, it should be.