The fuller version of the first quote is:
"For me, I read the script that Alex [Kurtzman] and Bob [Orci] wrote, and I genuinely loved it. There was this thread running through it. I think what happened was, through the pre-production, production, and post-production, when you have something that works as a whole, and then you start removing portions of it—because there was even more of it than was in the final cut, and everything was related. Once you start removing things and saying, 'No, that doesn’t work,' then the thread is broken, and it’s hard to go with the flow of the story. Certain people at the studio had problems with certain parts of it, and ultimately the studio is the final say in those movies because they’re the tentpoles, so you have to answer to those people."
He then said, "I’m proud of a lot of it and had a good time, and was a bit taken aback by the response."
I said earlier in this thread (on this page, I think) that, after watching the deleted scenes, I thought they picked the wrong things to keep (should have cut more Max Dillon and kept pretty much everything with Gwen or Harry they cut). I'm glad Andrew Garfield agrees. A simple different cut would have made a big difference in the reception to this film, which I still love.