an intellectual threat? as in, writing a mean review about the player character's latest monograph?
That would sure scare the crap out of me. 
I completely disagree. You haven't even given reasons as to why they're poorly written. These are villains that are roundly heralded so you'll have to have more than "they're not well written" to make any sort of argument.
Well, in the case of Saren, he starts out pretty much as a cartoon villain ("AAAAARRRRGGGHHH!!!!!!! This human must be . . . eliminated."). Then all of the sudden, when it's revealed that he's indoctrinated, we're now expected to feel bad for him because . . . why? The emotional arc of the character makes no sense at all. As for Loghain, he was fine I guess, although I admit that because I'm not terribly invested in Dragon Age, I haven't thought about the character as much. I played about 10 minutes of Dragon Age II, so I don't know a darn thing about the Arishok.
I cannot think of a single female villain I would particularly call well written.
Making an effective villain often depends on making use of very primal emotions and concepts such as fear and power. These are not things that can be politically enforced. Although that kind of reasoning is probably above the heads of people whose brains shut down at immediately speeds whenever the issue of 'equality' arises.
If a villain is intended to be intimidating, it's probably best to stick with a man.
Seriously? Not one in the entire history of literature, film, theater, TV, games, etc.? Ever? Sticking with cinema for a bit, how about Norma Desmond from Sunset Boulevard, Phyllis Dietrichson from Double Indemnity, Lady Kaede from Ran, Nurse Ratched from One Flew Over the Cuckoo's Nest, etc.? I could go on for a while here.