The biggest problem were the movies the cast and crew wanted to make and the movies the studio wanted to make. You can tell Webb, Garfield, Stone, etc. wanted to make movies about loss and grief and how people can move on from such things. Sony wanted the Spider-Man version of Nolan's Batman films and then wanted to launch their own pseudo-MCU based around Spider-Man with the sequel.
What they should have done was cast Stone as MJ, and cast another actress as Gwen if they were so insistent on doing The Night Gwen Stacy Died.