I'd really like to see a martial arts/melee skill tree and fist weapons.
I saw someone mention Naginatas, I think they would be a good addition, they could be part of the spear skill tree or their own tree.
A long range skill tree to add different skills for the bows and guns. Not sure what or how, but I just think it would be fun to have a long range build.
The ability to recruit NPCs you've met to help out in missions. Sometimes it can take forever to summon someone. I think it'd be cool to pick someone you've met, like Hanzo, to be your partner in a mission instead of only being able to summon other players.
I'd really really really like a third item wheel. There are so many different items that you can find and unlock that only having 8 available really limits what I can do. I currently have my elixir equipped in both wheels so that it makes healing easier so really I only have 6 free slots. Having so many different useful items but only being able to equip 6 means I have to backtrack or find a shrine to add them, and then into my menus to equip them if I want to change something. This is kind of cumbersome and as such I really only keep the same setup, and have a large build up of useful items that are just too situational to give up my slots for. Adding a third wheel means I could have one wheel for items, one for ninjitsu and one for onmyo magic.
What are some things you'd like to see added?