Ultimate X-men #2
Okay, I have to give some credit here. There are some good ideas in this issue. If you want to make some changes to the character of Wolverine, why not start him off as an assassin for Magneto? I really liked the idea of the Weapon X program being an offshoot of S.H.I.E.L.D., heck there are way too many unauthorized organizations in the regular Marvel Universe.
It also gives the mutants a real fear of humans by showing them that if they piss off enough of the wrong people, they actually could be slaughtered. Granted this issue, pretty much tosses characterization out the window, in order to fit more action, but ultimately ( no pun intented ) it turns out to be a strong issue.