I feel TM was perfectly cast for SM1 because you get a equal glimpse of both the nerdy Parker and the heroic Parker, both of which Tobey portrayed magnificently. I think Tobey's performance was good in SM2, but that his character was written perfectly to suit his comic counterpart. The third was also pretty good, but the direction they put his character in seemed to skew away from the what the first two portrayals had created. One can easily argue that MJ and Harry were done well in SM1, but didn't seem the same in the sequels. The possible reasons for this would be either the actor/actress did a lousy job, or the creative team did a lousy job at characterization.
In short Ladies and Gentlemen of the Board, the problem does not lie in TM, but rather the way the character is written. I think each of the actors did the best with the script and lines that they were given, and if there was anything wrong, it begins at the root of the movie, which is the script. After all, it's not like they have Stan Lee or any of the other comic writers for Spidey writing the scripts for the movies. They have Hollywood writers who write for live action. Big difference between between the two, so obviously the character is going to be written differently too.