Possibly. However, the fact remains that the majority of the HERO system line is dedicated to Champions. It's HERO's biggest selling setting and the one most synonomous with the system. D20 has become a universal system of sorts, but would you suggest deleting the Dungeons & Dragons 3.X and Star Wars Saga threads and lumping them all together in a generic D20 thread? Or a better analogy here would be to move the M&M forum to a D20 thread.
I think the key here is that for the most part, Champions and HERO System are just about used interchangebly, despite the fact that HERO is a universal system, like you said. Most people use HERO for Champions and will instinctively go to a SuperHero thread rather than a Universal game thread.