I definitely prefer Peter doing things on his own, which we got to some extent with Parker Industries, but I think SHIELD could have been cool as a change of pace. Though I guess now that I think about it I don't think it would work all that well after maybe 10 or 15 issues. It sounded better in theory than it would in reality IMO.
Why? Being a super genius has been part of his character since the beginning, and it's been constantly shoved down our throats by the writers that Peter could be like the smartest person on Earth when he grows older and if he gets more time to apply himself. Personally, I'm glad they finally started to deliver on that promise - now, all there is left to do is for them to not forget about it again. As long as the science/tech/intelligence doesn't overshadow the more important aspects of Spider-Man (the responsibility, the guilt, and the heart), then, IMO at least, the more the better!
TBH I still struggle to see how Peter was ever an "everyman". Even when he was a teen and written by Stan Lee, he was far from normal. He was an outright social outcast (which the normal person is not), completely awkward (which the normal person is not), a super-genius (which the normal person is not), went from being extremely unpopular to extremely popular with girls (which the normal person is not), an orphan (which the normal person is not), etc etc. He always was extraordinary. I hate this stupid "everyman" myth which Marvel uses as an excuse to stop Peter from ever growing as a character or being written well. I think it all started with writers with a poor understanding of Peter's character in the early and mid 80s (ex. Peter dropping out of college was one of the stupidest moments in Spider-Man history).