We are always talking about characters but where are the arenas wishlists?
There should always be a Lin Kuei stage and a Shirai Ryu stage in every game, IMO. Same with a Shaolin stage. Make the Shirai Ryu garden/grounds stage outside their dojo, nice and colorful just like in the comic. The Lin Kuei one can be indoors this time.
D'Vorah's lair, full of spider webs and all sorts of other nasty shit, could be pretty awesome. Now that she's enemy #1 in Outworld and on the lam.
Somewhere atop a tower or mountain, with lightning and wind storms, where Raiden and Fujin can have an ultimate showdown of ultimate destiny. Wink wink nudge nudge.
Rain's palace, or wherever he hangs out in Outworld.
Noob's sanctum, or wherever he hangs out in the Netherrealm.
I'd say some Edenian stages or a Red Dragon base, but it doesn't look like they'd be very appropriate to this story.