It's tough to say considering the Wii U ports muddy the waters a bit. There's a few key franchises that haven't had Switch original titles but they do have old ports.
Objectively speaking, I'd say that the biggest absence in the Switch's library is an original 2D Mario. Mario Maker just isn't the same, and U Deluxe is a seven year old port of the culmination of six years of the very samey NSMB series. Personally speaking, I am incredibly curious what direction Nintendo will take 2D Mario in a post-NSMB era.
I'd also add Switch original Donkey Kong and Mario Kart titles despite the critical and commercial success of the Tropical Freeze and 8 Deluxe ports.
As far as my personal biases go, it has, is, and will always be, Pikmin 4.
If I was forced to choose one that is completely absent from the Switch entirely though, I'd go with Star Fox. Aside from the Wii, Fox and Friends have made an appearance on every Nintendo home console since 1993. Hopefully the magic of the Switch does its work and the franchise finally takes off. Rhythm Heaven is also very conspicuously absent; much in the same fashion as WarioWare I can't see developing a new title eating up a ton of resources so I'm surprised it hasn't happened yet.