Link's Sword (Or the Master Sword)
The Monado (The sword from Xenoblade, look it up. Sorry, I'm a Japanese game hipster.)
A Fez. (To complete The Doctor's outfit.) Crossbow or Bowgun (From the Monster Hunter series) (The difference from bows would be that the arrows fired wouldn't be affected by gravity, higher damage etc etc.)
Chainsword. ('Cause Phaseblades ain't messy enough!)
Craftable simple guns and ammo. (Instead of refining weaker bullets.)
Cthulhu (Boss, obviously.)
Russian Army Outfit.
A special gun that only fires special ammo.
More NPCS (Sword and Armor dealer, material dealer etc)
Zipline. (to reach floating Islands and to get back down quicker.)
Aaaaaaaand so on...