the majority of those who aren't:
the mandarin,
another iron-themed/exosuit villain, or
mandarin's son
haven't been seen in who knows how long, especially not going after iron man. maybe he DID have a bit of a rogue's gallery, albeit they sucked for the most part, but he's hardly had anyone in recent years. sure, it's probably partially due to civil war and becoming the head of shield and this and that, but he's been fighting very few supervillains solo for quite some time now.
Even though you're talking about mainly Wolverine, I'll throw out some OK X-Men villains...
I've always had a fond spot for Apoc... but my general dislike of Trick has made me seem to hate him, Gladiator, Mr Sinister, Bastion/Master Mold/Nimrod/Sentinels, Sebastian Shaw, Danger, Cassandra Nova, Stryfe, Mystique, of course Blob... I guess I should add Vulcan, and Phoenix to it, meh.
I'll go with other on this one. Thanos has a great rogues gallery for a villain of mostly iconic marvel heroes: Adam Warlock, Thor, the Silver Surfer, Drax, and Captain Marvel.