Mully, you can't be so fixated on "team talent". After nearly 30 games, it's the school's resume that determines their seed, not how fast their pg is.
But you have a valid point about the crapshoot. I've often been in the NT as (for example) a 3 seed, looked at my bracket and gone, "Man, I wish I was the 6 seed". Ideally, that sort of feeling shouldn't be prevalent. But I don't know how to guard against it without majorly and blindly favoring the BCS schools, and I don't know if that's such a good thing.
In the end, I truly think if they made tweaks to the two issues I mentioned -- quality of wins/losses over total W/L and the current overemphasis on CT performance -- that it would help stop this from becoming a real issue.