It was NOT due to his storytelling and his writing, which for at least the first year or so was very strong. I mean, yeah, he went too far with that Spider-totem stuff, and he was the one who had Spider-Man actually EAT Morlun, but that's not what I really had in mind.
I think that he matured him too much. He made him a teacher, he developed the marriage and relationship with Mary Jane (And at the time, I think that Joe Q and Marvel were trying to break the two of them up and try to get around the marriage.), he changed the relationship between Peter and Aunt May, and he was an Avenger during his run. He pretty much made Peter an adult, so he changed him in a good way. He even wanted Peter to have kids (Sins Past. And after Marvel said no, that story should NOT have been written!). But then they had to go back to the status quo and reset everything back. Joe Q wanted Peter and his characters fresh for a whole new generation, and I think at the point we realized that Peter was never going to get out of the status quo. So, in a way, I think that JMS ended the series. I think that they should have ended it there, and just rebooted the series, like DC did with Superman back in the late 80's. So, this is not really due to JMS as a writer, in some ways he was perfect for the character. But maybe he shouldn't have been able to make such changes in the first place. Grant Morrison seemed to have the same problem with his X-Men run. I pretty much consider OMD the last Spider-Man story.