I've read various theories, but I usually just like reading fan reviews of the CDs. Some of their reviews are very insightful.
A surprising number of people didn't realize that Malice Mizer kept making music after Gackt left (or that they had a vocalist before Gackt). As for why Gactk left, Gackt has talked about it before and I believe there was an interview about it with Mana and Kozi and they all kind of kept pointing fingers and so it's likely the world will never know what truly happened, unless you asked an unbiased intern who was bringing them tea and just happened to be a fly on the wall or something. I like to think that the members have already patched things up between themselves or are in the process of doing that, but that's between them. We may never know about that, either.
Fans can be pretty scary, though. I remember watching a Gackt live performance with my friend where he started doing... questionable things with the microphone stand and all the comments were things like, "...I wish I were that microphone stand..." I think the song was Fragrance, which makes me think the mic stand was rubbed down with Axe.
(My friend watched the Brise performance on the Merveilles DVD with her mom, but her mom kept saying "Why are his pants unbuttoned? Did he forget to button them? I just have this maternal urge to rush onto that stage to button his pants!" Knowing her, I know she'd do it.)