I think the auto-cook system could be as simple as double clicking on an item in your recipe book
One thing that I'm really hoping to see a mod or patch for, and i know this has been brought up before, is a "memo" system on the map, and the ability to view other areas on the map, instead of just the one you're in. I can understan why a vauge map system could make sense in this game, since it's not as if she can just pull out her map and scribble a fuw notes in it. But, I think for a game like this, where new areas can be explored based on new abilities and items, it's useful to make a note of any possible secrets and barriers, so you at least know to go check them out at the end of the game. I did that a lot in Phantom Hourglass, and it made the whole process of item collection a lot less frustrating.