Nintendo already confirmed you can plug in the GBA games to transfer over. Even the older games had methods to counter having Pokemon that were super strong early in the game. In LeafGreen, you can't transfer Pokemon from Ruby/Sapphire until you defeat the Elite 4. In all the Pokemon games, I think that if you don't have a certain badge, monsters over a certain level will not obey your commands. So there are methods to counter-act having super strong Pokemon early in the game.

You can get all the previous 251 Pokemon in Ruby/Sapphire by linking up with LeafGreen/FireRed.