Oh, it's okay. I understand your point. But like, I'm the kind of guy who will pick out game mechanics that aren't consistent with story, make fun of them for a bit, then just enjoy the game. It's not even a black mark on the story in my opinion, it's just fun for me to do... but darn it, I can't do that with your games! Figured you'd have done that on purpose, but I guess not. Only in my little crazy world developers would do that.
And, you are absolutely right. You don't need a vague story for the sake of future game mechanics. Who seriously actually cares if all of that is completely consistent? I mean, I guess you get cases like certain JRPGs where character deaths can't be healed by in-game death-healing items. You also get a bit of a sense in a game like Diablo that, if there are as many heroes as there are players, why do YOU have to be the one who stops Diablo? Same way with story-based MMOs. You, deep down, know that you aren't the special hero some may call you... but they still call you that anyway because that's the story not meshing with the way MMOs work.
But like, I always think it's cool when there are little explanations for game mechanics as part of the story. Any game where gameplay and story mesh well get bonus points in my book. Bastion is damn good for that.
Oh, and I'd heard about the Star Trek technobabble thing before. Unfortunately, not being a respectable nerd (kidding), I know only very little about Star Trek. But the way you make it sound, it seems a lot like House got to be after a season or so. The medicine took a backseat, it was already simplified enough, all for the sake of drama between characters and such... then again, it's not compelling viewing worrying over whether a patient is going to live or die... most of all one you don't particularly care about.