The reason people don't like it is because your choices have NO consequences what so ever.
This is spot on.
You end up building an alliance, allegedly 'leading' an army, becoming a Jedi Master (and sitting on the Council by the end), and having numerous 'choices' of how to deal with people...
... All of which have no consequences whatsoever. You can't do anything to make your 'army' stronger, in fact you can't even use it; they do nothing other than act as scenery in your quest cutscenes; it exists purely for the benefit of dialogue.
You gain no perks for being made a Master (that Master's Retreat from the beginning of the game? Yeah, just an empty building with nothing in it); hell NPCs don't even react differently to you depending on your rank or repute other than in sycophantic quest dialogues.
All in all, it could be rather grandiose and wonderful, but it's not. Bioware has succeeded in making a game in which your actions and choices go entirely unrewarded and without consequences in reality, other than affecting what a quest NPC says to you in a cutscene dialogue (and sometimes not even that). I ended the Consular story feeling entirely unfulfilled - cool, I now sit on the Jedi High Council. Except, I don't, do I? Not even in my own single player way. Even my companions don't acknowledge it.
Frustrating and unfulfilling.