Where is my Phoenix Wright Amiibo.

perv!

Metroid and Pikmin are quite violent franchises. How many games do you know where you drag the corpses of creatures you kill back to your spaceship in order to breed more Pikmin in?

But they own Sonic and Rockman ... ?

No. Thats why they have to have Capcom and Segas permission to make them...

Pretty sure they had this deal set with Capcom and Sega during smash's development. Bayonetta and Snake aren't in smash. And in Snake's case not even is present on the system in any form, so it benefits neither Nintendo nor Konami.

Well I would like it if Nintendo did have amiibos for a more mature audience, but highly doubt it.

Of all the exemple you mentioned, no. But not because they are violent but because they are not theyr IPs. None of them are owned by Nintendo. With maybe the exception if Fatal Frame that I think is only partialy owned by Nintendo. But if Bayonetta was in Smash or owned by Ninty, absolutly. Same thing fort Snake. As for Fatal Frame I see it as extremely unlikely even if it was fully owned by Nintendo, but not because of it's violence but because it's not nearly mainstream enough.