I gotta weigh in on this because among our local gaming cadre this has been a topic of heavy conversation for a while now and I'm glad to see it on the internets.
We've all had the same feeling the OP has for a while now. I'll focus my discussion on Mass Effect, but know that for us at least it represents RPGs as a whole. Mass Effect brought fantastic new technology to the RPG genre, but in exchange for almost ubiqitous voice acting, better blocking and technical direction for the onscreen characters, and a massive upgrade in the quality of the look and feel of the environment you ended up with a lot of sacrifice.
Sure your "choices" carry over, but what effect do they really have? There are some different characters you interact with, but otherwise you're on the same rails that any JRPG sets you upon. Not only that, but for all the improvements that are made the invested time to deliver them is robbed from the production of actualt content. How many hours of real storytelling was there in Mass Effect vs Baldur's Gate 1?
And I think storytelling is the key here to the feeling that many of us are getting not just about Bioware, but the RPG genre in general, as was suggested by another poster. Somewhere along the line Role Playing Games came to be synonymous with Levels, Exp, Skill Trees, and Phat Loot. I can even pile these upon the plainest, most undeveloped characters and call my game an RPG now. I don't know who decided Role was now your summary of mechanical calculations and not your world view, personality, or even approach to other characters, but I condemn them. The qualities that cam to define Role Playing Game are largely lacking in the new RPG genre since your choices really only determine some other number attached to your character, whereas the outcome of the story is always decided beforehand.
I find myself astonished that a decision I make has any effect on the world at all in most games now. It's an amazing event, which is a sad bastion of greatness in a genre in general decline for me. Sure Mass Effect has a higher number of these moments than many other games that have been released in the past decade, but being the biggest brine shrimp in the pickle jar still means you're just a sea monkey, no offense to sea monkeys that may be reading this.
Sure, many jump to the defense of many of the recently released products. And "Well I still find it fun." is a VALID argument, don't get me wrong. But that doesn't mean that I can't continue to hold many of these companies, especially given the standard they set for themselves, to said standard or an even higher one. And I think some of us are doing just that. Further I think it's our right to set our expectations too high and have them dashed. As long as we're civil when we discuss it, no harm no foul.
Which brings me to why i was compelled to even post. I was so glad to see a forum post on one gamer's opinion of Bioware, and that there were further posts by those who agreed and disagreed, with none of them resorting to attacks. I was so moved to see this that I HAD to post on this magical oasis on the internets where no trolls and no flames wars preside!
In conclusion I'd like to toss out that NWN 2 was actually developed by Obsidian (used to be Black Isle), not Bioware. The same goes for KotOR 2. Further, I attribute most of my RPG favorites to Obsidian (Black Isle) as they've demonstrated their ability to produce characters, events, and choices that resonate with me and leaving me with the feeling that I Played a Role in their story Game. And I fully support them when and where I can.