Edenia and Outworld were two separate realms.
There is no real consistency with the eye colors other than looking cool and intimidating. Mostly they do however indicate that the character is dead. One day I was thinking that maybe Hotaru was under a spell of Damashi → would explain his odd behavior and inconsistent eye color.

The artists are just inconsistent. They can't keep the designs straight from one game to the next. The worst offender is easily Mileena, who originally had the same eyes as Kitana because they're supposed to be able to pass as twins, then she had white eyes in MK Gold because she had died and come back, then she had normal eyes again in Deception for no good goddamn reason, and suddenly in MK9, she has Tarkatan eyes, ruining the whole "twins" thing completely.

I'm also pissed that they changed the Shokans from red eyed to yellow eyed in 9.

To answer a couple of your questions more specifically though...

Baraka's eyes were never black, in MK2 and 3 you couldn't actually SEE his eyes, they were deeply sunken in, hidden by the shadow of his brow, that's what made them look "black". John Tobias's concept art always depicted them as RED though...until the first time we see them in-game, in MK Gold, where they look yellow with slit pupils, and that's how they've looked ever since.

Reiko's eyes are glowing blue because Noob Saibot's eyes glow blue (or they did before MK9...though they still do in his Retro costumes), and Reiko and Noob have similar powers and backstories (both are undead who work for Quan/Shinnok), they're probably the same kind of undead.

(Originally, Reiko was going to BE Noob, but the devs decided they wanted to make a new character instead and created Reiko, using some of Noob's character model and special moves.)

Intersesting stuff. Thanks for the replys. I'm unimpressed that they can't follow basic designs from a previous games (such as eye colours). We'ed be pissed if Scorpion went from wearing Yellow to pink, so why can't they do the same with basic face and body design.
MK9 may be a let's hit the reset button, but there are alot of unanswered questions that NRS are just flicking the fingers at us and not answering. Such as why is Quan Chi wearing Shinnok's madelion. Meleena just being created when originally she was thousands of years old and so on.
Big thanks for the Baraka explanation about his dark eyes. Just thought he had black eyes, never thought about shadow.