I'm not sure I totally buy the criticism, in part because I just haven't played enough Bioware games to really be able to see the comparisons (KOTOR and BG2, the two I played, seemed to have strikingly different characters). It also seems like the same criticisms can be lobbied against the PS:T vs. NWN2 and FO:1 vs. FO:2.
For Black Isle/Obsidian, for example, we could list:
The hardbitten female tiefling thief with a tumultous past relationship.
The wise but inscrutable gith spell-caster with an uneasy bond with the protagonist.
The beautiful, winged "dark angel" cleric, emotionally scarred, surprisingly naive, and often tender.
The scarred outlaw with a dark and secret past for which he's trying to atone.
To the extent Obsidian characters don't repeat prior instances, they're often stock characters like the noble, surly animal god, the angry dwarf, the arrogant and bookish wizard, and so on.
I don't need to do the same analysis for Fallout, I assume, because everyone's familiar enough with the tropes.
To be honest, what I find more annoying is not the use of well-established general tropes but the need to give each of them a "humanizing twist." The desire to have it both ways (for example in the NWN2 OC) is often especially excruciating, as we're expected to assume that a single childhood trauma of some sort gives "depth" to a cookie cutter character. Frankly, I think I might actually enjoy playing a game that had the Evil Wizard, Noble Warrior, Vulnerable Princess and so on if they were just straight-up executions of the archetypes (a la Conan).
--EDIT--
I'm also fairly sympathetic to the idea that at least some games should be designed as wish-fulfillment vehicles, and most gamers have as their highest wish to be the heroes of bad, cliche fantasy stories. Sad statement about the world, but there it is. A relatively small number, I would think, what to play psychiatrist to a lunatic ward of alien creatures or the mediator in the midst of uncomfortable social drama.
--EDIT 2--
I also think that it's not unreasonable to have most of your fighter-heroes be men, rather than women, when you're relying upon a historical milieu in which women wouldn't plausibly be able to do the kind of fighting that's taking place. Now, maybe the answer is that if men can carry 15' swords and wear preposterous shoulder armor, women should be allowed to fight as if they had adequate upper body strength, but the fact is that the idea of a "woman warrior" has been freakish historically (like the Amazons or Fa Mu Lan) not mainstream. I don't think every fantasy story calls for such exceptionalism.
So if you've got a game that's mostly about killing things in a medieval setting, having the women do their killing with magic rather than melee weapons isn't, in my opinion, sexist or close-minded.