If Samoa Joe and AJ Styles moved to the WWE, I would like to see AJ Styles head to the Smackdown Brand and have Samoa Joe head towards the Raw brand.
The Smackdown Brand is the better show for great wrestlers who could produce weekly quality great matches and AJ fits the mold perfectly. AJ Styles would definitely play a babyace and would fit the Upper Midcard / Main Event department on Smackdown. I could easily see him having great feuds with the likes of Christian, Cody Rhodes, Daniel Bryan, Wade Barrett, and possibly Randy Orton if booked right.
As far as Samoa Joe goes, I'd place him on the Raw Brand as a heel, just like he is at the moment in TNA but actually winning matches and being booked seriously and more dominantly. I think a monster heel Samoa Joe would help the Monday Night Raw roster greatly in terms of having more credible heels and depth in the heel department. I could easily see Samoa Joe having fantastic feuds with the likes of John Cena and WWE Champion CM Punk.