I like Bioware games, I've played all of them except for TOR (because: MMO), they're on my short list of devs whose games I buy/play when they first come out, and they provide a high quality, polished-if-bland experience with a combination of action and roleplaying.
Having said that all that, there are numerous reasons why Obsidian games are consistently superior to anything Bioware has put out.
1. Bioware reuses structural and narrative elements repeatedly. 3 of their games (NWN, KotOR, and Jade Empire) are nearly exact retellings of the same story. It's safe, people like it, but it also comes across as intellectually and creatively lazy. On the other hand, Obsidian games are ambitious both narratively and mechanically. New Vegas is probably as close as anything in their catalog to being what I'd consider "safe" and it still managed to push the envelope of what is possible in a Bethesbryo game.
2. Obsidian stories, while arguably better written on the whole, provide a more fulfilling narrative experience because they emphasize the player's interaction with the story through real choices and consequences and non-superficial relationships with NPC's. NPC's in Obsidian titles provide the player with feedback on how he/she is playing the game, and come with fully fleshed out personalities, opinions, alignments, weaknesses, etc. that the player can interact with or manipulate. Bioware NPC's exist for the purpose of handing out sidequests, conforming to RPG archetypes, and satisfying awkward nerd sexual fantasies. In Obsidian games, the NPC's encourage roleplaying by behaving in believable ways to the player's dialog choices and in-game actions, creating intrigue through a system of influences and alignments. In Bioware games, being nice to people means you get to boink them later and/or they help/hinder you in some way. In Obsidian games, if the player does have a major impact on the world (New Vegas), the repercussions of his choices are widespread and varied. In Bioware games, you have a good ending or a bad ending, occasionally even a multi-colored ending, that reflects whether you chose the good dialog or the bad dialog.
3. Bioware games are epic fantasies where someone rises to a great challenge that threatens to destroy the world. Obsidian games are games about the player character's growth and generally limited impact on the world. In Bioware games there is a great evil that needs to be destroyed or aligned with, in Obsidian games the player deals with personal challenges that primarily center around the player character.
