To be fair, Mario's Time Machine was not developed by Nintendo. That's like counting Faces of Evil/Wand of Gamelon/Zelda's Adventure against them. Although, maybe we should...
Harmonix probably shouldn't be eligible, I agree.
Treasure made Stretch Panic. If you want to argue that Stretch Panic was actually good, well, good luck...
Not familiar with that game actually. I will hunt it down and then revise my opinion accordingly. Probably won't change anything as I am a blind Treasure fanboy, but I might start to silently agree they shouldn't be included in these lists.
What about Mario is Missing? Its hard to keep track of what they are directly responsible for, and what was just a bad licensing decision.