Well if the Anti-Registration side has Batman then the Pro-Registration side is screwed since Batman knows the weaknesses of pretty much every superhero on the planet.
Yeah, but the pro-regs would likely have enough material on Batman to take him down with them or simply counter his weakness exploitations (seriously, if Ra's Al Ghul and such can take him down then it can't be that hard for guys like Reed Richards, Tony Stark or Nick Fury).
Seriously, this Batman Marty Stu stuff really gets annoying after awhile. One thing the merged world would do is increase the number of guys at least as smart as him.
Also, as we saw in "Infinite Crisis", Superman was willing to reveal his own ID to the government when McCarthy was doing his witch-hunt so there is some precedence for him willing to make superheroes accountable.
And besides, I think to Diana and Clark they wouldn't be against the idea of superbeings actually being held accountable for the damage they cause and other stuff.
Hell, Superman himself may be slightly less admired this time around by everyone. Things like Secret Invasion would make the populace less enamored of aliens, especially ones that look just like humans already.
Would Magneto use metahumans as further proof of how beings like mutants are destined to eventually be the new humanity?
The High Evolutionary, love to see how HE'D react to this whole thing.
The Legion of Super-Heroes, well maybe the Shi'Ar Skrulls and Kree are in place of the Khunds in the future.