What about for Mudkip candies? Mudkip might be the rarest of the Gen 3 starters (considering I've only seen one, so far), maybe Swampert could be your next project. I hear Blaziken and Sceptile are also worth the investments, as well. You can also save them for when Bagon and Beldum begin appearing in the wild, too, and for when Gen 3 legendaries eventually are released.
Do you have any other legendaries that you haven't powered up yet (Moltres, Entei, Lugia, etc)? I pretty much use my rare candies on legendaries exclusively, since candies are very difficult for me to come by for them.