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Unless a store is doing a promotion, you never HAVE to preorder a Pokemon game because they always have plenty of them out.
As of right now, no stores have said anything about bonuses sans Target which gives you a $5 giftcard on pickup of the game.
In the past, TRU has always been my go-to place because they've been consistently having something for releases since HGSS.
Target has had something for "main" game releases (ie, DP and BW) but nothing else.
Gamestop usually has nothing or they try to pawn off the free download Pokemon as your "bonus" (they did this with Victini, Genesect and Keldeo)
Walmart I'd doubt will have anything, but they just recently got their preorder cards back so..eh..
If I had to make a wager, I'd say that TRU will more than likely have this Power A stylus set with Xerneas and Yveltal on it. They had stylus sets for BW and HGSS and it's cheap enough that they can easily bundle them in when people pick up the game. I hope we get some sort of conformation though; with BW2 we had no fucking idea until like a week before release when we found out that TRU had the coins and UK GAME stores had the B/W-Kyurem DS cases.