I can't really offer an alternative explanation, but I have trouble believing that most publishers avoid Nintendo consoles purely because of the stigma attached to them without doing the calculations to see if there is money to be made. I know Nintendo platforms are notorious for getting less third party support, and the simplest explanation is that Nintendo games sell to the detriment of everyone else. Is Ubisoft just able to port their games more cheaply than, say, EA or Activision?
EA is hit or miss with Nintendo. Criterion being able to work longer to get out a better quality port of Need for Speed is a nice move. However, EA's not bringing out Madden or Tiger Woods PGA Tour for Wii U this year. Activision makes so much money off of Call of Duty, that it can easily take the risk of porting it to Nintendo home consoles. Although, we have yet to hear if the next COD title will be headed to Wii U. There's not much of an excuse to be had due to the transition to next-gen since Activision even put Call of Duty on Wii back in 2006 and Wii U in 2012. I'm not surprise by Ubisoft's support for Wii U, but I don't expect every game to hit Wii U. Ubisoft's just willing to be more supprotive of Nintendo platforms than some of the other big western publishers. It reportedly said that it wasn't that expensive to port Assassin's Creed 3 to Wii U, but that kind of goes without saying.
Ubisoft said this statement about Wii U development costs back in July 2012:
Out of seven games we are planning to launch five games are ports, so those are games for which there is a quite small reinvestment to do.
Ubisoft indicated that Wii U ports cost around 1 million euros (a little over $1.2 million). According to a 2010 report from Ibis Captical, a research firm, the average Xbox 360/PS3 development costs were $15-30 million. A $15 million title needs to sell around 500,000 copies to break even (not including overcosts). Double that amount for $30 million titles. As for Wii, the average game costs $5-7 million. If we go back further, the average Xbox and PS3 development cost was said to be $3-5 million.