I saw the movie for the third time last night (first on the IMAX - even better that way) and I totally agree that the Smallville running scene could just not be in the movie at all. The drowning scene could have been much shorter or yeh, not in there at all b/c Superman starts drowning 5 minutes later and its sad-music drowning overkill. I think some daily planet stuff could be cut out, and I agree the stalker scenes should have been totally cut out. Someone else (on imdb I think) came up with the idea of Richard and Lois inviting Clark over for dinner, and I was thinking last night that may have worked alot better. I actually like the heist scene/Kitty rescue scene alot, though I dont know if the gattling gun scene before it is relevant to anything. Mini-Metropolis does indeed drag, and I think thats my main gripe with this movie, is that it could have been much tighter, editing-wise.
I dont think I needed those Krypton scenes in the movie b/c they may have bogged it down even more, though I would love the option of an extended cut along with the theatrical on the dvd.