Every time you want to do the main quest, you are forced to join the Blades and to become an imperial agent, working for the empire (some NPCs in the main quest remind this to you, sometimes). For my next game, I'd like to play a character that gives his allegiance only to Morrowind people... Is there a mod to become the Nerevarine and to do the main quest without becoming an imperial agent?
No, the backdoor quest with

in the vanilla game is not enough. I want to catch the corprus, to get Moon-and-Star and to become Hortator and Nerevarine without joining the Blades.
And I don't want to join the Sixth House. So, mods like "Sixth House" and "Great House Dagoth" are not what I'm searching for.

By the way, would it break the lore if a mod makes the Nerevarine become a native from Morrowind?

I swear starwarsgal just posted a thread asking this same question...

Technically, yes. You must be an outlander to fulfill the prophecy. That's why most Ashlanders don't like the Nerevarine prophecies.

Well, not just posted, it was http://www.gamesas.com/topic/1472664-idea-main-quest-without-joining-the-blades/, but yeah. Basically, there isn't a mod that does this yet and the closest thing we have is Nerevar Say Nerevar, which makes Jiub do the main quest. If you care about continuity though, this breaks the lore for Jiub provided in Dawnguard. There is also no equivalent mod for Tribunal or Bloodmoon.