First of all, backwards compatible means it would work backwards on Wii. I know what you meant, but that isn't what BC is. I bet the Wii U version WILL work on NX, just like TP on Gamecube works on Wii and TP on Wii works on Wii U. So what difference does it make if they make two versions? Buy the one you want and quit getting upset about minor differences.
Second of all, because that is how they get money out of stupid people. People who think it matters. Expand sales by selling it to people with Wii U & selling a port to NX buyers that they will convince themselves is the better version so they can justify buying NX at launch so as to not have the inferior version even though they are the same aside from minor tweaks.
They don't need to make two versions. There is no reason. They may not even actually be making two versions, but if they do, it is solely because they want to maximize sales. Just like how the Wii version of TP sold so well on Wii and not Gamecube, because "oh my god, motion! New system".
It is because Nintendo is a business. They do not care. It is literally that simple. That is why.
Also, what are you worried about being better? Graphics, a few extra polygons that don't change the game? Controller differences? You really think whatever potential changes would be significant enough to really make the game "better" on NX?