Yes. Not that there weren't some decent storylines here and there afterwards, but the whole Siege Perilous/Reavers/Australia/Gateway/X-Men are dead/etc. nonsense is definitely where the title officially jumped the shark.
This.
There weren't too many bad storylines before Siege Perilous/'dead X-men', but there were fewer good ones afterward.
I agree that turning SO many villains to heroes was overdone. Magneto I get, but not every villain has a conflicted personality. Also, If someone started a topic on use of clones as a poor story crutch, x-men would be one of the biggest offenders.