There are lots of indie ones actually, I see them pop up on Steam often enough.
I never played these games much myself but my most favorite is Metaball which was a free Unreal Tournament 2004 modification. It had a cool dreamy atmosphere that reminded me of Nights into Dreams in some ways, it also had hints of the 3D Mario game design with the way the camera angles change at appropriate places within the same level for example. It was quite pretty and clever and had a hub world and in the actual levels various different types of challenges like speed, platforming, navigation/exploration in the more open environments, puzzles, operating devices other than your character/ball, whatever. You also had to change between ball materials of different properties to overcome certain challenges. Overall it was a really good package but sadly it never gained much traction with the UT2004 mod fanbase. I think it was going to be remade as an indie game at some point or get a sequel but it never came to be in the end.
There aren't any good quality videos out there, I guess it was before youtube was all the rage (or at all?) but I found this guy's playthrough, it has the wrong aspect ratio and he's also playing quite dumb in parts even though he's finished it before these videos (so you don't see the intro or anything even if you start at part 1).