Maybe in term of story telling some of those Phase 2 films were stronger, but Avengers is arguably one of the top 2 or 3 CBM's of all time, so I don't agree that any of the Phase 2 films were better. But yeah there were some weak links in Phase 1 which is understandable as they were getting their feet off the ground.
The two worst films MCU has produced IMO has been Thor TDW and TIH, and of those I actually like TIH a little better. TDW isn't a bad film by any means, they just had a terrible director, and it's sad they had a falling out with Patty Jenkins because I think it would have been a better film. Alan Taylor is a TV director, and while some of those guys can make the jump from small screen to large (Joss Whedon, the Russos), Alan Taylor seemed out of his league. The biggest problem with TDW is that Anthony Hopkins just seems like he was upset through the whole film and was just dialing in his performance. When an actor of that stature seems like he's board or collecting a paycheck on a film of that nature, you know there's a problem.
TIH was the other film that I think had a very weak director, but I actually like Norton's performance, and I actually like some of the rooftop chase scenes in Brazil. But overall it was a far superior Hulk movie to Ang Lee's disaster.