My new speculation based on pokemon gba weirdnesses...
Ruby and Saffire don't link up with old gameboy games, therefore nintendo wants everyone to start over...
sounds to me like they are getting ready for a mmorpg pokemon, because one of the problems would have been people using their 5 year old ultimate pokemon...
Only 202 of the 350 some odd pokemon are obtainable in both ruby and saffire, and rom people have looked into the code and found out that the two games do have the capability of having those missing pokemon in them....
Final verdict...
Pokemon mmorpg to come out very soon and you must play it online all of the time. It will have extensive link up capabilities with ruby and saffire and that will be the "one player mode" when your character "goes on vacation"
Yes its all speculation....but ya know...