The best according to.... ?
Herein lies my issues with inter-fed cards, tournaments, etc. See, someone has to run it. And that someone probably has conflicting interests. In all likelihood, they run a league with people in it, or are a part of certain leagues, and would like to see those leagues do well.
Does that necessarily mean they'll "cheat"? Of course not. Furthermore, they may honestly believe that the guys in their league are the best. Heck, the guys in their league may actually BE The best. But one of the big issues we always have with this is that whomever is running it has a tough time being impartial, whether they're favoring their own guys too much or trying so hard to appear impartial as to screw over their own guys.
Anyway, I don't know anything about the Cup. But those are my two cents about interleague events and tournaments and all that. That may just be a Prodigy old-schooler looking around and seeing a lot of people going in entirely different directions, and going from being one of the "mainstream" guys to one of the "niche" guys. But hell, what do I know.
Good luck, though.
-Josh