My opinion: Most of the real soul of the band died with Cliff Burton. I think they had an energy together that was lost. I think that Jason was a different kind of soul, but in a sort of spiteful dislike of Jason filling in for Cliff, James never really got tuned in to Jason and the band lost cohesion.
Or to put it another way, James tried to leave Jason simply playing backup to his rhythm without giving him an ounce of credit, but Jason Lars and Kirk don't make "Metallica." Even all four of them don't make "Metallica" like it used to be, but it might've been a better one if they had worked together more closely.
I think that James got a little headstrong and started leading the band in different directions without Cliff there to be sort of a musical counterpart. I think the band has always been mostly all about James and Lars, but I think Cliff was able to bring that extra dash of originality and musical creativity to make them great.
But I also consider other contributions. They got older. The whole musical scene changes and grows. Bob Rock. Growing popularity with mainstream success.
There's not really one silver bullet. But all bands have a "prime" period. I don't see why everybody has to crap all over their newer stuff just because it's not as good as the old, or not what they like. Just applaud their older stuff and move on.