And what reason was that? Length?

Some of these deleted scenes are great.
There's a number of reasons, primarily length. A lot of the stuff that was cut was kind of unnecessary and they wanted to keep the story moving.
The pizza delivery sequence, the scene with the Usher, and Peter's visit to the doctor were shortened to keep the story moving. We don't care about Mr. Aziz, the Usher, or the Doctor, we care about Peter. So they kept Peter's story moving.
The Birthday scene was cut short because it was more effective to leave the tension between Harry and Peter open. Plus, the audience is smart enough to know what the deal is between the two, so there's not really a need to dwell on it.
The scene with MJ and her friend was cut, because we get the same idea non-verbally that MJ doesn't love John in the scene when she kisses John upside down.
The action sequences on the side of the building and the train were shortened for budgetary & time constraints. Plus, Spider-Man should not be able to withstand getting smacked by a train.
The elevator scene was just an alternate take. Though it was funny, the one they used in the theatrical release was better.
Peter taking off his mask in the car after webbing up the crooks, I'm glad that was cut. Why would he unmask himself the middle of a busy street?
And the scene with J.J. in the Spidey suit, although funny & semi-creepy, was just unnecessary. It didn't need to be there to keep the story moving.
I like all the extra stuff, but I definately understand why they cut it.