From photos and concept arts shown to us in magazines and the Krypts, we've seen and learned things about characters and that were drastically different with what we see now. Some examples of this include...

-Jax's original name being "Kurtis Stryker";
-Cyrax being the intended new model for Scorpion;
-Havik being the new model for Noob Saibot;
-Darrius being the new leader of the Red Dragon;
-Reptile wasn't supposed to have as many changes in DA as he did, but were added on thanks to inspiration from Tiamat;
-Kintaro not meant to be a Shokan, but a tiger-based character;

There are several more, including different costume designs, alternate abilities, alternate storylines, different names, and even different characters altogether. My question to you is would you have prefered if some of these initial difference (not limited to what I wrote here) were kept in the final designs?
My own thoughts...
I think that the Cyber-looking Scorpion would've been a first step in branching him away from the ninja look he had had for the last two games (similar to Sub-Zero being unmasked). Rather than having him become a cybernetic spectre though, it could've been a new demon form for him to take on, and with a few colour changes, like adding more black and keeping the spear as a thrown projectile as opposed to it popping from his chest, it might've been an interesting change.
I didn't like the fact that Reptile had a flimsy tail in DA. If it had been a bit longer, bigger, and useful in combat, I'd have prefered it more.
Dairou's original story about being involved with the Deadly Alliance and having his own mummies to control would've been better than what he had in Deception.
Kintaro's former look was definately not one that I prefered, and I'm glad that he's now a Shokan creature.
Havik shouldn't exist. When I saw that that was going to be Noob Saibot, I thought that that was the coolest look he could ever had. The all-black ninja look has been his since MK2, and it's gotten stale to me, and I was disappointed when I saw that they used this costume to make Havik.
I'm not sure if this counts, but I remember a strategy guide had story possibilities for the returning MKG that were actually scrapped and replaced with what we now know, but I liked the idea of Baraka actually being killed by Kung Lao's hat and being ressurected with staples keeping his body together. It showed that Kung Lao's hat was more than just a prop for in-game use, and it demonstrated that when characters are ressurected, they needed their original bodies to come back. Plus, being held together by giant staples sounds neat.
Another concept that I thought was cool was Blaze's looks and fighting styles. An idea for him was to have hair on his head and have a unique weapon style of double axes (of course, the double axes now belong to Nightwolf in Deception).