Yeah, I agree. And I think the important thing for football in particular, is to maintain the uber importance of regular season games, while also providing a playoff to somewhat mitigate the controversy of deciding a champion.
It's interesting, there were some debates last week about the early season Duke match-ups (Duke vs. Louisville; Duke vs. Ohio State). On one hand, it's great to see those match-ups of two very good teams prior to conference play... on the other hand, the losing team really isn't dealt much of a blow at all (IE: It's sort of meaningless for the most part).
I agree with everything you are saying here. As great as March Madness is and it's my favorite sports event, it comes with diminishing the regular season. Pre-conference play is pretty watered down to begin with, even conference play, teams like Duke/Kentucky are almost assured making the tournament, they'd have to really play down to their talent level as opposed to college football, where teams like USC/Alabama aren't assured of anything, one loss even in the new format and they could be out. This is also one of the reasons I am/was against the additional WC spot in baseball since I want the playoffs to be as exclusive as possible.
I'm probably in the minority on this and doubt it would ever happen, but going down to 40 teams wouldn't be such a bad idea, I'd have fewer automatic bids though. And as we've seen in recent years with George Mason, VCU, and Butler as well as early losses by Kansas and Duke, seeding doesn't matter as much as it once did IMO.