I agree with your two problems with it and add a few more:
-Continuing the X3 problem of introducing a bunch of fan favorite mutants with no depth explored on screen. Between the first two X-Men movies, you saw so much of Wovlerine, Cyclops, Jean Grey, Storm, Rogue, Professor X, and Magneto and those characters stuck with us. Heck, even Iceman stuck around in our consciousness. Plenty of characters, but we got to see them and they actually mattered. You had some good villains in the second movie as well, but the third movie and Wolverine just seemed incredibly rushed when it came to introducing characters and then never seeing them again except for a five-minute fight scene, where they were gone in an instant yet again. They were just kind of...there.
If you had to narrow down the list of MAIN characters in Wolverine, they would be Wolvie, his love interest, Stryker, and Sabretooth. You could have made a much better movie with just those characters as the focus rather than introducing all these characters that are just there to advance the plot in a superficial way.
And to contrast this with X-Men First Class, the characters with real substance included Professor X, Magneto, Mystique, Beast, Sebastian Shaw, Angel (not the real Angel but whatever), Moira, and Havok. You could probably throw Darwin into that mix too with his heroic sacrifice (Azazel, Emma Frost, Tornado Guy, and Banshee were SFX budget users as far as I'm concerned). That's 9 out of 13 characters that had some memorable traits about them. This "introduce a bunch of mutants" thing CAN be done well so that everyone serves a purpose. Wolverine just kinda failed in that respect. Hard.
-Doing nothing with Gambit. He flies a helicopter and that's it. Okay, he does it twice.
The character fans were constantly clamoring for inclusion in the movies...and he barely does anything.
Okay so most of it was one big problem that also plagued X3, but still. Its heartbreaking to see memorable characters like Juggernaut, Deadpool, and Gambit just being thrown to the wayside like that.
@Bosk: as far as continuity errors, X-Men first class seems to have ignored that Wolverine and X3 ever happened, which is a good thing as far as I'm concerned. If they made a Deadpool movie that did the same thing, I'd be totally cool with that. I also agree with Dimi that Ryan Reynolds is the perfect choice for Deadpool.