Oh my god, I'm actually putting something in here. I'll probably forgot I did this and not look again for a week or something like always.
Anyway...there's a difference between being used a lot and something being overcentralizing.
I will use the Ferrothorn example somebody brought up in here. Yes, it is on just about every single team ever made, but it is far from overcentralizing when it is scared off by pretty much anything that COULD have a fire move or a fighting move. Whereas something like Latias really is only scared of random stuff like for example Scaqrf Special Lucario using Shadow Ball or something dumb like that [probably not close to a OHKO, but you get the point].
You basically HAVE to run SpD Jirachi or Scizor, two pokemon that could be 1000X more effective used in a different way, if you don't want your team to get smashed by Specs Latios. THAT, to me, is what makes something overcentralizing. When, no matter how good your team is, you basically NEED to run something in order to not lose to something that is simply a hit and run pokemon. Yeah...that's overcentralization at it's simplest.