Well, they've certainly left us enough in their lyrics and interview comments to speculate.
Although this is all conjecture, my opinion is that Stevie and Lindsey were just downright incompatible. I think they had a musical and physical connection. But I also think they struggled with power dynamics (i.e. both wanting to be "in change" or in "control"). Lindsey seemed to be the very jealous/possessive type, and I don't think Stevie is one to tolerate that ("what you did not need was a woman who was stronger"). I also think they were very competitive with each other, and I don't care what anybody says, too much competition in a relationship is never a good thing. Like the quote of Lindsey's about them never really being friends, even though they were lovers. I do think he was crazy about her (and let's be honest, what guy wouldn't have been) and was crushed when they broke up, as evidenced by the bitterness in some of his lyrics.
As for John and Chris, the booze obviously and tension of being in the same band, which has been mentioned.