bkev said:

Opinions?

Quite probably. Judging from all the hype about "secrets" in the theater, a subplot was probably deleted. I don't think it was too much of an overall detriment though. The story seemed relatively straightforward albeit good in its theatrical format. It'd be interested to see an alternative extended version on BD.

In my mind, there are two possibilities for cuts:

Negative Reception by Test Audiences- This still happens. Since the studio was hyping up the secrets, audiences really expected satisfaction from a believable revelation. Perhaps the test audiences thought that the suspension-of-disbelief was stretched too far, especially if the secret was that the spider gene was already implanted in Peter by his parents, as suggested by some trailers. I personally wouldn't like the idea that he was destined to be Spider-Man; Peter seems too much of a pawn that way.
Too Long a Length- The studio may have gotten cold feet because of the length. The movie was pretty packed as it is, with both an origin story, a fleshed out romance, and a really fleshed out villain. When I saw it, I remember people thinking it was long. With the deleted footage, it may have just been too too long.

Anyway, that's just my two cents. On the topic of Spider-Man, I hope the sequel adapts this from the original comic. They did set it up that villain during the end credits:

See that's what happens when you go on breaking promises. :-P Thoughts?