Considering the Mario Kart 8 bundle is coming out 2 weeks before E3, we can rule out any Wii U revisions. After the Direct yesterday went out of its way to show a great a deal this new bundle is and why everyone should be buying Wii U's for Mario Kart 8, Nintendo is pretty much betting it all on that game. If they're planning on this bundle improving the Wii U's current situation, they're not going to announce anything that could possibly make people hold off on buying it when the Direct showed they want as many people buying Mario Kart 8 between May 30's and July 31st, since that's how long that free game download deal will last.
I could see it being some kind of 3DS revision since the 3DS sales have been down this year in Japan compared to what they were last year. I wouldn't be surprised if they even release it this Summer to go along with Smash Bros 3DS, since that would be the most effective way to improve 3DS sales in Japan as quickly as possible. Plus we're kind of due for a new handheld revision since it's been almost 2 years now since the 3DS XL was released. Nintendo handhelds usually seem to get their new revisions every 2-3 years so getting a new kind of 3DS shown wouldn't exactly be out of the ordinary compared to what the GBA and DS had.