I have nothing to add to this technical hoo-ha. Also, I'm late to this podcast party - but at least now I'm all caught up. Anyway...
Disappointments in gaming - what a perfect question for an Internet gaming fan site! I'm surprised that hasn't been brought up sooner.
Twilight Princess disappointed me for sure, but of course it had massive, long-term hype (and the disappointed have already made themselves well heard/read by now). In addition to James' Temple of Time "wow moment," I thought the final real dungeon, the one in the sky, was wicked.
Wind Waker's clear omissions of dungeons were pretty disappointing, too. The third pearl and the fire and ice arrows all "should have" had dungeons. It makes you wonder how much better the game could've been had it had more development time.
Also, I got Yoshi's Story when it first came out for my birthday. That was a sad birthday.
P.S. Did Jon say "It's pretty Nietzche" instead of "It's pretty niche"? I think it was at the part about FF on VC...