Having one game library across all hardware sounds dangerously similar to Sony's port-heavy "console on the go" strategy with their handhelds, and would make it far harder to convince people to buy more than one Nintendo device. Indeed, judging by how the WiiU has been selling compared to it's competition, it seems that even offering unique software built around different devices isn't enough to mitigate that issue. People outside Nintendo's core fanbase seem more than happy enough to just go to the 3DS for their Nintendo games and leave it at that.
I really don't think this strategy is the slam dunk you make it out to be. To me, it seems more to be a necessity borne out of limited resources/manpower--the strategy they've come up with to avoid the constant delays that plagued the WiiU in it's first year. Nor would it mitigate the issue of Nintendo missing out on key third-party software, as several people have pointed out.
Have some time to kill? Read my shitty games blog. http://www.pixlbit.com/blogs/586/gigantor21