Although this thread will never have an answer, it has been brought up by many people that you cannot consider the JLA/Avenger's book canon. Sure it's canon for DC since they went forward with a storyline directly from there, but did Marvel do the same?
Any other comic crossovers come to mind that reflect the same kind of one-sidedness shown with this crossover? Image/DC come to mind. After all, whether you're a fan or not, Spawn's good ole shoelace face was provided by none other than Batman in a crossover by Frank Miller. Spawn sported the look for a while in Image. You think Batman thought twice about his fight with Spawn where he got his ass kicked?
So forget the canonization argument. It doesn't work on many levels. Respected writers? Highly touted and anticipated crossover? Same thing happened in Spawn/Batman. One side considering the crossover canon is as nonsensical as Spawn/Batman and is too self-serving to be considered authoritative.
I mean seriously... what the hell happened to Superman's weakness to magic anyway? Busiek pissed off a lot of people with that one. honestly, how the hell do you explain that away? Oh... its god power... not magic... err yeah... two totally different things... yeah... -.-