I guess you'll see that everywhere, to be honest. I see that on art sites as well, for instance - draw a [insert popular anime/char combo of the moment], and lots of people will be drawn to it and say it's great simply because it features their favorite char or whatever. It really just depends on preferences, and, I'd say, on a certain degree of... not sure, "maturity/experience" perhaps? Some will give top marks for these same reasons - because it's an anime they like, a song they like... Some will also give top marks because, well, they don't always know better, and haven't always really had the opportunity to compare with really good AMVs. Some will go past this and acknowledge both the merits and flaws, even if it's using footage from an anime they love. It all depends.
Anyway, the way I see it, aren't we here to make the vids we like first? It's not like we can sell them, become known in the professional world with them (as, well, it's not terribly legal, after all, using anime we didn't create and songs we didn't compose), and so on. If people don't like them, tough. If they like them, power to them. Even if the AMV next door using footage from the same anime has gotten better marks, as long as we like what we do, it's already some kind of reward... I think
