1. The Wii U uses a different architecture than other consoles, and most modern PCs. The Wii U is based on IBM's power pc. It's not necessarily more difficult, but since most third party games run on x86 architecture natively, it means extra work to port.
2. The Wii U has less ram than either of the other two systems. This means textures and such have to be compressed further than they would on other systems.
3. The Wii U is simply less powerful. This means certain effects have to be altered or taken out completely. Probably not for Elliot Quest, but in general...
As for Elliot Quest, it's not a graphically complex game, but it likely has a small budget and a small team, which makes altering the game to run on the Wii U might be challenging. They also didn't say explicitly it was a technical issue. There are also licensing issues and other red tape with the eShop. All of the console shops tend to be more restrictive than Steam.