I don't agree with you at all. Sure it would be very time-consuming to implement something of this caliber but this is not something that should be done anytime soon. The Devs can take as much time as they want to do this after they have implemented all the 'necessary features' for PokeMMO.
The 'Clone Pokemon' could be made far more rarer than Shiny Pokemon so that only a very few players could even think of having a chance encounter with one of them. Also, they wouldn't affect the Shiny Market in any way if they were untradeable now would they?
All in all, in my opinion, this would be a very fun addition to PokeMMO.