spoiler (click to show/hide)
It wasn't Magneto and you're better off just ignoring all the Xorn/fallout of New X-men.
Honestly, the quality after Morison and Wheadon takes a nose dive. You should pretty much ignore things in X-men and Uncanny that come right after that because they are shitty. X-men gets a little better with Mike Carey, but good in the sense of standard super hero stuff. Stuff happens, but honestly the core X-men books have been meh since Wheadon and Morrison.
There is X-Statix which is amazing and completely stand alone. Complete with character's only relevant to that story. Starts in X-Force 116.
While the core Xbooks have been kind of meh imo you have the Craig Kyle and Christopher Yost X-Force which is fun. Then the Rick Remender Uncanny X-Force which is also great fun. It does tie into lots of lore though.
And of course Peter Davids X-Factor is always pretty good.
I don't think you really need to read much before to understand Morrison's run. It of course references things, but I'm not going to ask you to read 75 issues of Generation X and some old Uncanny X-men just so you can understand where Emma's problem over dead students comes from. it's stated and you get it already. Likewise, do you need to read late 90's X-men stuff and Dream's End--a very throw away arc-- to understand Geneosha? Not really.
Really, to understand Morrison I guess reading some old Clearmont is helpful, but even that not mandatory.
Also the original Age of Apocalypse is good with the only real weak part being the Gambit series.