To add to this (thaaaank you, forum 3000 character post limit)...

If this is really your passion in storytelling, really the story you want to tell in a game, then it honestly may be that this is not the game for you. Clearly you are unhappy with the story and the game, and the truth is the game is not going to change to suit your desires in the story. I hope you find the game that does suit you and which you can enjoy.

FWIW, though, making a private server for an existing MMO as you mention does not generally allow you to significantly change the storyline, because the dialogue and cutscenes and whatnot are all part of the client. And unless you have the source code for the client, duplicating that side of things is far more difficult than reverse engineering the servers. If you really want a divergent storyline, you'll do far better to start your own game company and make an MMO.

And if that's the path you choose to follow... more power to you! Make the game you want to play, one where there's no good or evil, just differing shades of gray and horrible choices to be made. It could be interesting, and maybe there's a lot of other folks who would like it!

I'm genuinely not being facetious or sarcastic here; the beauty of the world is that there's always space for someone else to try telling another story of their own. (Whether or not various other people like that story is a different matter, of course.)

Good luck, either way, and I hope you find the game you're looking for out there.