I'm reading up. The only one I have a real concern with is item-dropping, but honestly on that, I think it should only be a part of the first two official quests and nothing else. It really should be implemented by scripting and limited to the 1st and 2nd Quest: I don't think anyone really wants this. Too many quests rely on corrected item mechanics and could break certain quests (I think New Quest and James Quest would be totally broken without Blue Earknut drops for example)
The other one worth noting is the side-warp bug (where you turn and go to the end of the screen), but if we're fixing the bugs I don't think this is a high level of concern.
Patra patterns might need to be fixed, but still, not too high on this as I'd consider this more an error on Nintendo's part and not so much an intended feature that he doesn't reset eventually.
10th Enemy Has the Bomb probably needs to be implemented in the 1st and 2nd Quests. 3rd and on, probably not, I'd leave it up to the developers.
-James