Hm... putting some thought into this:
Scorpion: A costume with him as Hanzo Hasashi, and maskless.
Liu Kang: Old school MK1 costume.
Kung Lao: updated version of one of the 3D MK costumes.
Sub-Zero: Updated Unmasked Sub-Zero costume (from MK3/UMK3)
Sindel: A more regal, less revealing costume.
Ermac: Not sure on this one, gonna have to think about it... something with him maskless.
Reptile: MKDA costume to troll everyone, lol.
Kitana: ...casual Earthrealm clothing. (but gotta keep the high heels)
Johnny Cage: Ninja Mime outfit
Jade: Light armor suit (she's a bodyguard right?).
Mileena: Well in the story some said she should be next in line for the throne, so a (less revealing) version of Shao Kahn's outfit may work.
Nightwolf: Business suit (as if he had gone into the whole gambling business and owned a casino).
Cyrax: The 3D MK's didn't have a bad idea with his alternate: half of the metal is gone so you can see him.
Noob Saibot: Noob could have a reaper outfit but not a skeleton, Saibot could have a slight variation on it, possibly his face is a skull. Both are maskless.
Smoke: Maskless, and more monster-like, like his arcade ending suggests he is.
Sektor: Similar to Cyrax.
Sonya: An actual military outfit, a real one.
Jax: Real military outfit for him too.
Kano: Prison garb.
Stryker: You know those good cop bad cop segments in movies where one of them almost always wear a white shirt with the straps to the pants (overalls?) and khaki's or something? Yeah that.
Shang Tsung: Hm... MK2 or MK3 outfit...
Baraka: MK Gold costume complete with the chest staples.
Kabal: I would say a costume before he was injured but that'd mean you'd have to make new win animations.... Holding this one off til later.
Raiden: like Samsung said, Christopher Lambert costume from the first MK movie wouldn't be bad.
Cyber Sub-Zero: Similar to Cyrax and Sektor.
Sheeva: Well she is of royal heritage so something regal and a lot less revealing just to balance out the other two costumes.
Quan Chi: Updated MK4 outfit.
Also: klassic kostumes for anyone I haven't already mentioned, characters that already have one, or characters with costumes that are really similar to their old costumes (like Kung Lao)