I'm not sure about having a "% of completion" badge, because a badge should be awarded for an actual achievement, not progress towards an achievement. Having a "(insert title here) Fan" badge might be ok though, depending on consensus.
I'll lay out how I think collections should be counted, based on my experience with the Mega Man series:
Separating NTSC/UC, NTSC/J, and PAL is a must. Each region gets different releases, with NTSC/J usually getting the most. Realistically, I think it would be easier if we just handled NTSC/UC, but I'm not sure how many collectors we have here that aren't North American. Certainly don't want to slight anyone.
Compilations should count separately as a single game. For example, I have Mega Man 1-8 on their respective consoles. I also have the Mega Man Anniversary Collection for PS2, GCN, and XBOX. For purposes of my collection, I would say I have NINE games in this instance, 1-8 and counting the compilation as a separate game.
One thing about compilations counting toward badges. Certain series have compilations of games which were never released in the States prior to that point, a good example is Gradius IV, it never recieved a release in the States until the Gradius III & IV set came out for PS2. Or Gradius Gaiden and Gradius II which never saw release until the Gradius Collection was released for PSP. These would need to be exemptions to the rule, since you can't get them separate.
This I agree with. Mega Man Battle and Chase was not released in North America. It was put on the Mega Man X Collection disc, so I consider that as having it. To make myself feel better, I also bought Mega Man Battle and Chase PAL and Rockman Battle and Chase NTSC/J but that's because I'm an obsessed perfectionist. But for purposes of collecting, I would allow the compilation to count separately only for those games that didn't get a specific release (so the compilation would cover Mega Man Battle and Chase and Mega Man X Collection slots on the checklist, but not Mega Man X1-6). Another example, Mega Man 6 was never released in PAL territories. I'd allow something like that to count a compilation or another region's release towards that (as I'm sure has to be done for Final Fantasy in the US).
Remakes are tricky. For example, there exists Mega Man: The Wily Wars, which is a remake of Mega Man 1, 2, and 3 for Mega Drive in Japan and Europe. I obtained the PAL release and a NTSC "pirate" conversion for the purposes of completion. I wouldn't count the "pirate" towards my NTSC/UC collection, but the PAL one should count. Again, I would count this as a single game, and not allow it to take the place of Mega Man 1, 2, and/or 3. Same goes for Mega Man Powered Up; I would count it as it's own game, not a replacement for Mega Man 1.
Obscure games go both ways. I wouldn't count Mega Man 2 and 3 for Tiger LCD to make a complete collection. I would, however, count Mega Man and Mega Man 3 for PC. A game like The Misadventures of Tron Bonne is difficult to place...it's part of the Mega Man Legends series, and not it's own game, but it doesn't have Mega Man in it. I guess a similar question is would you consider Luigi's Mansion a Mario game? I really don't have an answer for this.
Greatest hits replacing a black label should be fine. Having everything CIB could be a different designation. Like with Mega Man (and most game series), getting some of the old NES/SNES/GB boxes is insanely expensive, so CIB is an almost unobtainable goal. But if you did get it, instead of your badge saying "Complete Mega Man Collection", it could say "Complete Mega Man Collection+", with the + identifying CIB. Or, we could set a threshhold, like if you had 9X% CIB, you could count it CIB+ (from experience, the boxes for Mega Man IV, V, and MM (GG) run about 400 dollars a piece, so it's like trying to get a copy of NWC). Again, up for debate. It might just be easier (and fairer) to have just the "Complete XXX Collection" badge without discerning if CIB or not.
And I think this should be a manually issued award. Users should have to prove they actually have these games to make the awards legit. NA has you submit photos of your collection to prove you meat the criteria. I think we should as well. Not saying people are dishonest, it's just cool to get to see what people have.