Yoshi's Story and Mischief Makers were not sprite based, both relied almost entirely on pre-rendered visuals. It was a weird time when new 2D games had to be justified by the moronic "2.5D" marketing tag line thanks to a handful of idiots the execs were apparently scared of who expected that every side scroller had to either ape DKC's visual style or use polygons in order to be considered legit. I was in high school at the time and the "2.5D" buzzword was very annoying, honestly, it felt like an apology every time I'd hear it or see it used in an article.
Also, Mischief Makers was my first Treasure game and I still adore it. I was totally sold on it after seeing clips of it in one of Nintendo Power's Fall '97 preview N64 VHS tapes they would send in the mail and also reading the review for it in Gamefan. I then waited about five months for Yoshi's Story expecting that to be the better game only to be gravely disappointed, Mischief Makers had so much more depth, variety and challenge. Funny how an independent small skeleton crew of ex-Konami guys ended up besting NCL. The Yoshi series wouldn't be fully redeemed for 18 years until Woolly World thanks to Good Feel who I sincerely hope gets to do every Yoshi game from now on.
Of course there were other good 2D games on the N64 like Goemon's Great Adventure and Kirby Crystal Shards but yeah, it was very sparse.
Edit: Yeah, pretty sure Bangaioh and that Puyo Puyo 64 game someone posted were the only games to use hand drawn 2D sprites, everything else was either pre-rendered or used polygons like Kirby 64.