Here's another crossover I don't know much about but I'm inclined to think favorably of because of a single tie in I read years ago.

So I take it that the idea behind Acts of Vengeance was to get all the major bad guys attacking the good guys en masse or something, right?  Either that or have the villains face off against superheroes they didn't normally encounter and hope for the best?

Well whatever the case, I remember reading Captain America's contribution to the series and being really impressed with a story that might never have been told had this event not come along.  I'm sure a lot of creators feel as if they're getting shoehorned into some awful, gimmicky, event designed just to fiddle around with sales figures for a month or two and try to make their involvement as painlessly tenuous as possible when it comes to these things, but Mark Gruenwald recognized the storytelling potential inherent in what had been handed to him and ran with it even if what had been handed to him made no sense.  Actually, scratch that - ran with it because it made no sense.

Often times, villains are put together with no thought as to whether or not it makes sense for them to be brought together.  Respected Businessman Lex Luthor team up with Serial Killer The Joker?  Sure, why not?  All you need to know is that they're the two biggest villains in the DC Universe and there you go (a similar logic was behind the decision to have Bane fighting through a crowd of superheroes alongside Doomsday for a scene in Infinite Crisis).  I don't know exactly how Dr Doom, The Red Skull, The Kingpin, and Magneto wound up together in the first place, but I suspect the idea wasn't "who would make interesting bedfellows for this storyline" so much as it was "let's just put the biggest names together in one place and see what happens".  At least one writer however, took into consideration the fact that although all these guys were villains, at least one of them was a Concentration Camp survivor and the other a Nazi.  Would these two really work together?  Apparently they would, but the moment their business had been concluded, Magneto asked The Skull for a moment of his time.  Telling him of his time spent in a concentration camp as a child, confirming that this Red Skull was the same one of half a century prior, Magneto made it clear that they were not friends and that Skull had better have put his affairs in order before entering the same room as he.

Buying none of this, Magneto treated The Skull as he would any opponent (actually probably worse)

To be honest, maybe this was the plan all along - use Acts of Vengeance to get disparate groups of people together who might appear similar to the reader and then have the writers explain how they're not - but it seems to me that Gruenwald took a powerful set up that perhaps few others recognized and claimed it as his own in a story so great I can't believe it didn't occur decades sooner.