Because assuming that if the Wii U has trouble with FE2, it'll have trouble with its beefier, more intensive big brother is not sensible?
People have already addressed the bit about why it works better with the 360 or PS3 several times in this thread and others. In the simplest terms even I can understand - power isn't evenly distributed. It seems that the Wii U's strengths don't align with the 360's/PS3's (and more importantly, what the FE needs the most), and this is evidently creating problems of some sort.
Are we seriously going the "This time, it's personal!" route? Really? Really?
EA is not in the position to take petty revenge against Nintendo (also, companies are not single-minded entities). That's just the fact of the matter. They're hurting for cash right now, and a lot of their big titles right now have performed well below expectations. It's in their best interest to get more games out there, provided there's a chance they will sell.
Do you seriously think EA would commit financial hara kiri out of some (mostly unsubstantiated, mind you) grudge?