Half-Life's Protagonist Was Originally A Dwarven Biker
Half-Life tells the story of bespectacled armored physicist Gordon Freeman and his battle against an insidious alien force. Far from looking like your traditional space marine, he looks more like Edward Snowden after not shaving for a couple of days. However, the character might not be so popular today if they had run with the initial character model (on the right):
"Meth: Not Even Once."
The early prototype by character designer Chuck Jones more closely resembled a perpetually surprised lumberjack making the minimum possible effort at a Halo fan convention. Before they settled on a name, the designers nicknamed him "Ivan the Space Biker."
"... AND MY CROWBAR!"
This wasn't just some drunken idea scrawled on a bar napkin, either, but the actual character model that was used for an embarrassingly long time, lasting well into the testing phase.
Finally realizing that a character who looks like he sells crystal meth behind Showbiz Pizza probably wasn't the best hook to hang a franchise on, the designers eventually decided to dial back the facial hair and gave Gordon a tasteful dye job and a pair of glasses. The model can still be found deep within the game's code, though it can't be opened without a little computer wizardry and an insatiable desire to see a more terrible version of your favorite game.
BioShock's "Little Sisters" Were Almost Giant Slugs (Or Worse)
BioShock is set in a dystopian future run by people who not only managed to make it all the way through Atlas Shrugged, but decided to base a whole society on it. One of the more terrifying aspects of the game are the "Little Sisters" -- brainwashed, glowing-eyed little girls tasked with running around the crumbling city and extracting genetic material from the many corpses littering the ground. When the player comes across a Little Sister, they can choose to kill her and take all her genetic material for themselves, or save her for a much less bountiful amount of material. This choice determines which ending you get when you beat the game.
None of the endings involve getting these poor kids some Visine.