An exploit that allows the Internet browser to use the latest version of flash, and also be update friendly. You'd be able to access Youtube without swiching software apps. You could do work from your 3DS, and even play flash games, emulating the buttons as keys.
An exploit that allows blocked Nintendo ID's to be erased, without the help of Nintendo. They don't assist everyone with the ban code, so I think it's just fair if it was developed for the less fortunate. It could even have a yearly limit. Like if you are misbehaving, you can get blocked again and this time have to wait a year. but good behaved people wont have to worry about that.
An exploit that allows Skyping through your 3DS system. One main reason I got a 3DS was to chat with others because my computer was down...well...Swapnote was discontinued during that time, and there were no other messaging places other than texting on your friends list...in front of everyone else. Soooo I think that It'd be amazing to have Skype messenger app.
....And a cupcake generator. I'm hungry.