One reason why there might be tensions between Webb and the studio is that the film seems to have been reworked significantly shortly before release:
I noticed some of these things as well as I was watching the film, but they didn't detract from my enjoyment of it too much.
Thanks for sharing that article, it's an interesting read. It did seem like a lot of the storylines were just cut short in order to fight The Lizard. Although maybe one way to interpret it is Peter puts his own revenge search on the backburner in order to protect innocents (but there should have been some reference, just a line indicating he's going to continue the search for Uncle Ben's killer).
The star tattoo makes me think that the killer is going to part of a group, perhaps tying into a larger arc with the villain of the next movie.
I hope those deleted scenes make it onto the dvd. I'd especially like to see more of Gwen and her father.
IGN had this article which speculates about what the end-credits scene means.
I've long championed Mysterio to be the villain so I hope it's him. Electro would be visually interesting as well.
His father is a strong possibility too given that storyline is going to span the next films.