I'm sure Nintendo will do the best they can. Maybe the graphics present a higher challenge to the cpu's than many other games and both portable and docked are 1ghz with only 3 cores available to games. Still more powerful than wii u.
Also if this is a heavy online game and the main cpu's are partly responsible for wifi processing that could be a reason. Mario kart is fairly simple with regard's online functionality but there will surely be a lot more data getting moved about with Splatoon. On the wii u they cut down the number of cars in online races because it didn't have the cpu power on need for speed most wanted compared to ps3 and 360. Online gaming is surprisingly cpu intensive.
wii u had a dedicated arm chip for its OS, nothing special but meant all 3 ppc cores were available for games and a dsp for audio (very limited with no compression functionality but got the job done) and I think its wifi chip had dedicated processing so wii u had some assistance from support chips. Most mobile technology often makes use of the main processors for sub tasks to reduce silicon size and improve battery life where its more efficient to have one chip doing multiple tasks than have a wide range of different chips doing different tasks.
One exception is intel with their atom chipsets which often rely on support chips and are not as popular as arm based designs. Intel weren't used to doing tablet chipsets and ended up having to dump their chipsets on the market probably at a loss probably because of this lack of integration. Just making the point that mobile chipsets often under-perform compared to their expected performance based on their specification. So I think heavy use of wifi is likely to erode some performance elsewhere.
