How will this work with BW/BW2 in transferring your previous Pokemon? Also, they are saying that this will help prevent cheated Pokemon from being transferred. How will they do that? Lastly, will Pokemon obtained from a BW/BW2 ROM on an R4i be considered as "cheat" Pokemon?
Together with the Pokemon Bank app you will get the Poke Transporter app. Load that Transport app when your BW or BW2 game is inserted and you will be able to transfer all the Pokemon that are in Box 1 on your BW or BW2 into a special transfer box. This transfer box can be accessed from inside the Pokemon Bank app. You can move them from that box into your X or Y game or into your Pokemon Bank boxes. It's just like the protection that is already on the GTS. Obvious cheated Pokemon, like Charizard on Lv 1, will be rejected. No, if it isn't a hacked ROM they should be considered as legal.
Right. The Transporter won't recognise the game which is on the R4. You have to bring your Pokemon on a retail copy of BW or BW2 for transfer.