Brandon's right on the nose. Bioware has always had character-driven stories. Usually the follow the heroes journey in various styles. They've played with it and subverted it, but just because you follow formula doesn't mean it's a masterpiece. Bioware is probably the better out there, but come on if you're expecting all of them to be awesome you're just going to be disappointed.
Let's say I agree with you. Bioware tried to tell a character-driven story in Mass Effect. I don't think that excuses the lazy copout of a story, driven by a deus ex machina ( yes, I'm aware it takes it to a literal level - I find it sad ), and having an ending so nonsensical that in ten minutes it took me from being a ME fanboy to having no interest in the series ( I haven't even tried the extended edition, which I think came out a little while ago ). Simply put, I don't think it's too much to ask for both good characters and a solid, coherent plot. It's hard to pull off, no doubt about that. But things that are worthwhile usually are. And the result is games like Heavy Rain, Metal Gear Solid, The Witcher 2, and ... not a whole lot more that I can think of.
As to why I don't necessarily agree with you about Bioware and character-driven stories, I just don't think their characters or their exploration of those characters is really that deep. Deep compared to standard action games, yes. But compared to deeply psychological games like Heavy Rain? Not at all. That may seem like an unfair comparison, but ... basically, tough shit. I don't buy that an action RPG couldn't tell a story with characters of the caliber found in Heavy Rain. It's just very difficult.
EDIT: AHHHHHH Metal Gear Solid 5 basically confirmed two weeks ago! Cancel Christmas!
EDIT2: I'm reading a lot of good things about the story in Spec Ops: The Line. I'm going to see what the hype is about.
Edit 3: Spec Ops: The Line seems like fun so far, and the story looks to be more interesting than the standard action game. It has some flaws, though. Weapons, in particular, are ... weird. Ammo is scarce, so I end up having to swap weapons quite often. It wouldn't be so bad if you could fire semi-auto, but weapons are full auto by default. While all weapons have alternative fire modes, for the M4 that's a silencer, which seems more or less useless. For the SCAR-H it's a grenade launcher. For the AK-47 it's burst fire - which is really weird, considering, to my knowledge, the AK47 doesn't have that option without being modified. It's a completely random choice, which is a tendency a lot of devs have.