I think it would be cool if they released the Oracle series for the 3DS, allowed you to pick which one to play first (just add a beginning screen like in OOT3D after you complete the first version), and then when you beat both, maybe unlock the Oracle of Secrets (I'm assuming that's what it would be named, as the series wasn't even 'Oracle' until they got rid of the third game). It would be a remake, as well as a new game, which would pretty much make everyone happy. I'm not even saying updated graphics or anything, but I do think that three linked games would be a lot easier now. (Make a save file, choose the game to play first, play it, then play the next, and finally unlock the third).
Or, even just for the eShop as they are, with the passwords. It would be nice if, since the 3DS doesn't play GBA/GB games, they released a lot of the bigger titles on those systems for the eShop.