Whatever Nintendo and EA's relationship is at the end of the day they both would like to make a profit. I don't know how much it costs to a port game to the Wii-U but if EA lost money on porting ME3 and they feel that porting games later down the line will only lose them money than so be it. Obviously this is all assumption for all I know ME3 U was a massive success.
As for Ubisoft I feel they are onboard with the Wii U, because they may lose money on a few ports early on but later down the road when Wii U owners start getting accustomed to AC, maybe Far Cry, Watch Dogs they may be more likely to purchase them down the line. But I'd rather not speculate, just this time.