Some of the reasons are I believe;
1. The wii while successful became seen as a poor console in retrospect not being able to compete with 360 and PS3 and missing out many important games or getting substandard versions. It became a niche console despite its huge sales.
2. The wii u lacked a amazing launch title that made people want the console. Later big titles came out but by that time the failure stigma had been attached to wii u.
3. The gamepad isn't very good to be honest. Not only is it over-sized for small children (a huge part of Nintendo's normal audience) but its lack of analogue triggers made it a retro step as a controller.
4. Nintendo hadn't made the console sufficiently powerful that it could outperform 360 and PS3. Most early titles performed worse on wii u than the older consoles and this would have been hugely negative to a wide audience. It really should have been something like 500 gflops for its gpu and something like a dual core x86 processor with a third powerpc core for wii mode and additional support. Something that would comfortable outperform 360 and PS3 even for launch titles. To simply have 3 low power ppc cpu's running at 1.25ghz made the console hugely difficult to match ps3 and 360 performance. Both those consoles are fairly cpu-centric.
5. The wii u was only really suitable for die-hard fans of Nintendo games for many of the reasons above and that simply meant it's potential audience was small.
6. Lastly weak hardware means its hard for developers to achieve much with wii u that hasn't already been achieved elsewhere. You can't really push gaming with such limited hardware. Something that really is now only doable with PC and PS4.
