If were going to start counting the games not coming because of that engine it is going to sound really worse than saying EA isn`t with Nintendo... again.
Supposing Fifa will come to Wii U, there are only 2 games i can think of that might seriously hurt Nintendo: Madden and BF 4.
Fifa aside, those are the games - i believe - really matter the most to gamers.
I can`t see a Madden replacement, but we don`t know yet if there will be or not a replacement for BF 4. Time will tell.