I'm going to go ahead and be controversial here: I don't see the point of either becoming a "true" leader of a faction or even creating one of your own. I suppose I can see the allure... I just don't understand what makes those mechanics fun in a single player RPG.
How do you make the day-to-day management of a guild fun without using infuriating Fable-like button-timing games to affix your seal to various documents or other such nonsense?
How do you make "giving orders" and "changing guild policy" meaningful in a game populated with NPCs?
Real organizational leadership takes a special mix of competency, inspiration, a knack for managing interpersonal drama, and leveraging people. In video games, people are not people, they're scripts.
Sorry, I just don't see how they could make that fun.
I completely agree with everything you just said.
Oh, and lets leave the good guild vs. evil guild out of this, and go back to how to was done in MW. Nearly every group was somehow intertwined with each other and had dynamic, instead of FG vs. BWC, or MG vs. Necromancers. There was 0 dynamic and choice inside the guilds in OB. In MW, you could aspire to be a dike, in-between, or a nice guy/gal within the guild and other organizations. Hell, the FG had a side that was completely corrupt, made you shake down people for the lulz, and was deep inside CT pockets. The Mages Guild had you sabotage other members' work, kill members who didn't pay their dues, had a leader who was wholly incompetent, and shake down anyone who taught magic outside the guild/kill the Telvanni (like what a real guild would do, keep its monopoly). The Thieves Guild had you steal from anyone your employer told you too, but also assassinate and blackmail people in the CT and FG. And that's just naming a few organizations, the houses are in even worse shape.