Don't own a Wii U, so my knowledge on its software library my be wrong, but doesn't the system have a decent amount of indie support in addition to a few console exclusives (Runbow, Freedom Planet, ect)?
The system is fine on the indie front, but the software echo system is very different compared to the Vita, which is in a similar spot the Wii U is in, only the situation is completely flipped (Nintendo: First Party and Indies but no third party games from publishers/Sony: No First Party Releases but a lot of indies + JP titles releasing on the console).
The Vita has indie games in spades due to how they are successful they are on the console; lack of major Sony releases pushed them to get a lot of attention in late 2013/early 2014 and the platform exploded from that point on for indie developers. They got a market hungry for games and they are willing to throw lots of games at them

.
JP publishers/developers did this too late 2013/a lot of 2014, leading to JP titles finding great homes on Vita. Point is the Vita community wanted indies/JP games and thus, more came.
Nintendo systems want Nintendo games, so games Nintendo-like (Shovel Knight, Fast Racing Neo, Freedom Planet) do very well on the console. Games not Nintendo-like, likely don't do very well on the E-Shop, but they do well enough to warrant more releases from developer/publisher.
Point is that the Wii U is getting indie games but its not getting as much compared to the Vita due to how Nintendo game sales eat up a good deal of sales from other titles. I could be very wrong stating that, and if people want to correct me, feel free to do so

.
But historically, third party games (which includes indie games) sell second to Nintendo produced products.