The problems have been said to be a result of interference by Sony producers, namely Avi Arad and Matt Tolmach.
Now in a recent interview with Amy Adams through Variety, Andew Garfield echoes those sentiments offering he was heartbroken over what happened with his Spider-Man where we see he mentions how great director Marc Webb was (meaning not Webb's fault, either).
I’m loath to judge that experience and paint it as a whole. But there were great things about it. I got to work with incredible actors and a really great director. I was very young — 25, 26 — and I felt young. I’d only done a few films, and I was feeling in the right place. I felt guided into it, and I knew it was the right thing for me to do. I learned a lot about what feels good and what doesn’t feel good and what to say yes to.
There’s something that happened with that experience for me where story and character were not actually top of the priority list, ultimately. And I found that really, really tricky. I signed up to serve the story and to serve this incredible character I’d been dressing as since I was 3. And then it gets compromised, and it breaks my heart. I got heartbroken a little bit.
Regarding how the Amazing Spider-Man movies got compromised, word first hit about the problems with Avi Arad and Matt Tolmach when the composer on the first movie came out and explained why he didn't return for the sequel. Composer James Horner said he had a great relationship with director Marc Webb, but the producers on the movie didn't want any of Webb's input, and that all Sony cared about was having "action" in the movie--meaning Sony didn't care for a good story or a good character, as we see Garfield mentions above.
The good news is that both Avi Arad and Matt Tolmach have seen their input "downgraded" (if they even have any input at all) for Spider-Man: Homecoming as Marvel Studios now has full creative control. It's said Marvel Studios president Kevin Feige was adamant about not having Arad involved.
The bad news, however, is that Arad still remains somehow connected to the Spider-Man property at Sony as he has been said to be behind/want the Spider-Man spinoffs with Venom, Carnage etc. Hopefully, Avi Arad has learned his lesson and realizes that simply having a product out because it's "something," ie just "Spider-Man," does not mean it will be enough to satisfy, but as Andrew Garfield suggests, needs a character and story as being the top priority.