I'm gonna regret getting into this...
Yeah, unlike the rest of GAF I don't actually think TPP is "awful". Flawed? Sure as shit! Not awful though, not by any stretch. At least TPP was consistent.
Shit no. MGS4 is the mess here. It's a flabby pail of self-hating swill that seems more concerned with hitting a check list of pander points than in saying anything even approaching worthwhile... well, not beyond how tired Kojima is of the MGS formula, at least.
Off the top of my head, the only story critical thing I can think of that was missing from TPP is a convincing lead up to Mission 46. SuperBunnyHop made a very astute point regarding how unearned that ending was.
As an aside, I wonder how many people would think TPP was incomplete if they hadn't put some of the cut content on the Blu-Ray...?