http://www.eurogamer.net/articles/df-hardware-nintendo-wii-u-reviewSoftware quality will undoubtedly improve over the coming months, but with Microsoft and Sony looking to launch their own next-gen consoles within the year, time is not exactly on Nintendo's side. One developer working on a key AAA franchise port told us anonymously that the Nintendo toolchain is "fighting us every step of the way", suggesting that plenty of work still needs to be done in getting development workflow up to scratch. Will the tools improve in time? Will publishers have the time and the financial incentive to stick with it?
Which seems to backup this post from wsippel over on neogaf that he posted months ago.
http://neogaf.com/forum/showpost.php?p=38426144&postcount=705An IDE is the environment you develop software in. The most common IDEs are Visual Studio (Microsoft), Xcode (Apple) and Eclipse (open source). A toolchain is basically a set of applications to translate source code to something the machine actually understands and consists of compilers, linkers, assemblers, build systems, debuggers, profilers and the like (often hidden behind or part of an IDE). The most common toolchains are the one integrated in Visual Studio, the one integrated in Xcode, and the stand alone GNU toolchain (open source). For Wii U, Nintendo decided to go with the GHS MULTI IDE and toolchain, a rather exotic and expensive suite that is typically used in high reliability, high security embedded development (like medical, industrial and military applications). It's simply not a familiar environment for game developers, most of which most likely never even heard of GHS, which means that it requires additional training and education
If true, then we know why ports are running worst than the PS3/x360 counterparts because devs haven't fully understood how to utilise the Wii U hardware to its potential and Nintendo going for an unfamiliar route.