..other than completely change the nature of the gamplay.

the first 2 U pad game will be absolutly no sooner than 1 year after nintendo's announcement to developers that 2 gamepads are allowed.  2 years for a high quality game.

But why would it change the nature of the gameplay? Of course its completely dependant on the game, but with the 2 cases I mention Fifa and Zelda battle quest the gameplay should remain exactly the same. Fifa uses the Pad for more accurate passing, shooting and player management during a match. How would this change for 2 control pads? 

Equally Battle quests has people with the pad take on the role of archer, including 2 archers will make very little difference to the game. 

my programing experince is outside the realm of games but i think this is sort of a universal concept.   when you make a fundamental assumption about what your program will do (like only support 1 player for the role of the archer) it takes a lot of effort to reverse that assumption late in the dev cycle.  i dunno, i could be wrong in this case but i'm going to get nintendo the benefit of the doubt on this one.

Well I would expect the more conventional multiplayer experieces to support it in the near future. COD, Madden, Fifa etc

In regards to nintendo specifically, i just think they are being overly cautious with the launch games in terms of their features. I'm sure if Ubisoft managed to get Assasins Creed running at 1080p, ninty could do the same for New Super Mario Bros U. Oh well...