Considering the giant corporations involved, there had to be some tough negotiations if Kingdom Hearts was ever going to be made. Disney was pushing hard for the game to star Donald Duck as the main protagonist, while Square kept lobbying to let them use Mickey Mouse. Meanwhile, Tetsuya Nomura stopped drawing zippers long enough to create a human hero wielding a chain-driven sword, a tail, and a Mickey-inspired wardrobe. Disney approved the initial design but thought the sword was too violent, prompting the invention of the Keyblade.
images via kingdomhearts.wikia.com
Consider the fact that Team Fortress' journey from freeware add-on to a freemium hat store took a long time (like Duke Nukem Forever long). Back in the far-away year 1999, TF2 was promoted as having a "realistic" military vibe and the testosterone-y title Team Fortess 2: Brotherhood of Arms. It wasn't until 2006 that the art-deco cartoony aesthetic we've come to love was revealed. Valve claimed that the release had been developed and redeveloped as "three to four different games" before being finalized.
images via wiki.teamfortress.com
Kratos' creator David "Zeus" Jaffe has talked about how the Ghost of Sparta was born out of a "feeling" more than a look or story. The goal was to make a strong-chinned annihilator through which players could unload all the rage and brutality that tends to build up during the average weekday. The team at Sony Santa Monica experimented with several looks including a few that seemed a tad out of place (though after E3 it looks like they never forgot about that 'Lone Wolf and Cub' homage) in Ancient Greece before settling on the ol' bald and chains.
images via wikipedia.org
Let's be honest, NOTHING in the NES Final Fantasy games actually looks like Yoshitaka Amano's concept artwork, so why would the franchise's iconic yellow megachicken buck the trend?
images via Secret_Wizard
Sega was aware that Bayonetta's gothic fashionista look and distinctly Japanese sensibilities was going to hurt its appeal in the West. That's why they hired concept artists to explore the idea of altering the character to make her more appealing to the "freedom and Chee-tos" demographic. The results were these Umbra Witches that were more rustic with a frontier sensibility.
images via massiveblack.com
Halo wasn't built in a day and it took the work of several artists to refine the iconic design of Master Chief. It's like a crash course in character design, without the hard angles and towering physique, you just have an unintimidating spaceman, not the single greatest soldier in the galaxy.
Dragon's Crown was originally meant to be a sequel to designer George Kamitani's 1997 game Princess Crown for the Sega Saturn. Alas, the late 90's was cruel to both 2D Fantasy-Action RPGs and Sega home consoles so the project was scrapped. In the intervening 15 years Kamitani got a bit more ambitious and the original character designs recieved significant "upgrades".
The original Borderlands game was rolling off the assembly line. A trailer had gone up, screenshots were released to all the gaming magazines, and the action RPG was going to take its place as another post-apocalyptic shooty-boom. Then it revealed a new art style that had the sketchy energy of a teenager's notebook. It's safe to say that this helped set it apart from Fallout, and gave them the chaotic sensibilities to pull off its more comedic sequel.
image via sigtutorials.com
The premiere source of ADAM in Rapture went through a few iterations. The earliest idea was a wide-eyed bipedal chipmunk guarded by a homicidal robot (like a horrible bizarro "Ratchet & Clank"). Eventually the idea of the Little Sister/Big Daddy dynamic was fleshed out but the sisters' design was still evolving, as you can see from the balding Gollum-like version above.
Images via bioshock.wikia.com
This character model (dubbed "Ivan the Space Biker" by fans) was indeed the initial concept for Gordon Freeman. Eventually the psycho-beard was traded for a goatee and glasses, but even then the Gordon we all know and love was given a douchey ponytail for a while afterwards, hooray for the '90s!
images via half-life.wikia.com