Oh snap, good choice, haha! Will rename him that.
Actually, it's not difficult to breed them for shiny, just can be really time consuming. As for Nature... When breeding with a Ditto, you initially breed the Pokemon you want to be shiny with a Ditto of the nature you want, if the original Pokemon isn't it already. So say, I want a Timid Froakie but my Froakie is Jolly. I would take the Jolly Froakie and put it in with a Timid Ditto. This Timid Ditto would be holding an Everstone. (These, in breeding terms, allow the Pokemon holding it to pass on its nature to the baby.) Then the babies would all be Timid rather than random. But if you were going for a Protean Timid Froakie, might take more since getting Protean might take a little time.
Improving IV's is easy if you have 6IV Ditto. Just slap on a Destiny Knot on the Ditto and throw it in Day Care. Destiny Knot takes 5 IVs (from both parents) and passes them down to their babies. You just replace the Pokemon you're breeding with one that has better IV's to keep getting higher up the IV ladder.
Edit: Just got a Timid, Protean Froakie that is 31/31/31/x/31/31 if you would like to try breeding one.