Well what a different going for 100% makes. The DS version was better early on but I found myself getting bored toward the end. The controls while better when played on the Wii U, still aren't the best for the later levels like Rainbow Cruise. I got all 150 stars, but the final 30 stars really do feel like bloat for the most part.
Went back and got all 120 stars on the N64 version after finishing the DS. When going for 100%, I'm back to finding the N64 controls to be better. The analog controls while still not the best when played on the Wii U at least, are much better suited for some of the harder stars. And speaking of harder stars, even though the N64 version was causing me lots of frustration at time, I actually prefer the difficulty over the DS version. While I like what it did with some stages like the Desert, they toned down some like the Clock level way too much. The Clock is actually one of my favorite levels in Mario 64, since it has some of the most pure platforming in the game.
Overall, I wont say one version is clearly superior to the other. The DS version does have a better camera and makes some nice changes to some of the stages. But on the other hand, I find the N64 version more fun to pick up and play thanks to the controls which are smoother and faster. The DS version adds more content but I found a lot of the new stars to not really be all that great. I liked new stage they added where you rescue Mario but none of the other new ones felt all that compelling. I wonder if because that's the only new stage that's you're required to play so they put more effort into it then the others. I didn't really mind the switching between the characters that much since not that many stars require a certain character, and they do give you hats to turn into Mario, Luigi or Wario in the stage itself.
If I had to chose, in the end I'm going to have to say I prefer the N64 version over the DS version. It was still nice to be able to finally play both right next to each other to compare them. Hopefully we'll get a remaster with more effort put into it someday that includes both version together.