I can see the "Ultra" version of those games having the National Dex(but the original will not be patched) and that being a huge selling point for those games, then people will go "See, GameFreak listens ;)" even if it was their plan from the start.
I doubt it, I think a Ultra version with small differences seems more likely. Such a depressing thought the Ultra games are going to be the most complete pokemon games for a very long time.