It's a good idea, there's been many times that I've thought about doing this. Only problem is the comments are stored in the .proj file that TF products (well...i'm pretty sure they are).
I remember when i first started doing CE I was commenting like CraZY cause i thought it was being stored in the ROM (yea...i was an idiot back then). So for the longest time i thought other people who were loading up the rom in TF were seeing my comments. Turns out I was wrong cause we were only sharing the IPS, not the .proj folder
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Anyways it's a great idea though i've found that the way that game does certain events is WAY over complicated than what any hacker would do. I think it's cause their events were tool assisted......um maybe an example would help:
I've found that many times when the game loads an enemy it sets pretty much EVERY value it can....for example sprite priority, speed, movement properties stuff like that. most of those properties aren't even used and you can usually get by with just loading the sprite. Why would the developers add this extra code? I'm guessing they probably had some sort of tool that loads up a map, and they can just like...drag and drop the enemies onto the map. And dragging/dropping would set all those properties for that enemy.
So if I were you I would comment, like....cutscenes which were probably closer to being coded line by line then other parts of the game. Things like loading objects and battles were probably automated and for our purposes it's probably better to check out the how-to thread.
--JP