Batman Begins wins this contest for me, without hesitation. While some folks had a lot of trouble with the third act, I didn't, and think the film really holds up on repeated viewings. It's a clear, focused film, with strong performances. It also has a discernible arc for the main character, and he's just as interesting as Bruce Wayne as he is in the costume.
SR had some high spots - gorgeously filmed, incredible effects, and two strong leads (Routh and Spacey). Routh, despite the snide remarks he's getting from some, did a solid job with the role and I bought him as both Clark and Superman. Having said that, SR is too meandering, adheres too closely to the 1978 film, and introduces some questionable elements (Jason Lane). Where SR fell down the most for me, however, is the lack of emotional connection with the story. I never cared about Lois, Jason, Richard, or really anyone else in the film except for Clark/Supes. Unlike the Bruce/Rachel relationship in BB, the Lois/Clark/Supes relationship was key to the film, and I didn't sense any chemistry or connection. I also felt like Bosworth was extremely flat in the role, and that the role was not well written.
It's a weakness shared by BB - Katie Holmes just didn't have the chops compared to the rest of the cast, and the part wasn't the greatest. However, it was a much smaller and less important role compared to Lois' in SR, and didn't negatively impact the film as much.
Despite the weaknesses and failings of SR, I look forward to the next film, and hope it's more of an original Superman story. I've been wanting the next Batman film since June 15 last year, but not for wanting better - just wanting more.
