Beginnings is still just a port, so it doesn't count.

Bayonetta franchise is not exclusive to nintendo seeing as how the first game is on Xbox 360 and PS3. Likewise bayonetta 3 has not been announced, let alone exclusively for nintendo.

I think you should take it off, or add metal gear solid twin snakes to 3ds and lego city undercover to wii u and other such exclusives.

Also, where is metroid prime for gamecube?

Also mario strikers for gamecube

Mario Strikers is not current, the next Metal Gear is coming to everything except Nintendo consoles, and City Undercover is a single game. Please read the OP. 

I'm debating if I'm going to count Prime as a seperate subfranchise of Metroid, or just part of the Metroid franchise. 

Bayonetta... shortly after 2 came out, interviews came about saying how Bayo's future would likely be on Nintendo. That being said, nothing has been said of that recently, so I'll strike it.

nice list. wanted to know what are the IPs/franchise that are still yet to come to the Wii U/3Ds.

I was a bit confused, but things make sense now. You are right on Mario strikers. Lego city I assumed would be part of the lego series, but I guess it is its own thing.

metal gear solid twin snakes was only on gamecube (my bad), and snake eater was only on 3ds (someone pls check my info), so I assumed that's 2 exclusive nintendo games within the same franchise, one of which is on the 3ds. Does that not count?

and I do think metroid prime is different from metroid seeing as how one is 3d and the other is 2d. Also metroid prime trilogy I believe is on the eshop for wii u .............. and metroid prime: federation force is coming on the 3ds....

The franchise has to be primarily exclusive to Nintendo, not merely have representation on Nintendo consoles. This list was made to highlight exclusive franchises on Nintendo, not individual games. If I wanted to be nitpicky, Twin Snakes is a remake of the original Solid anyway, and Snake Eater was originally on PS2, later on PS3, Vita, and 360.

I suppose I could split Metroid Prime and Metroid, though I would probably also have to split New Super Mario from regular Super Mario under that same logic.