It’s easy to pick your least favourite character but think about story development. if there ever is another Half-Life game after Episode Three, who would be missed the least?
Personally, I say kill them all except Gordon and start a whole new story arc. Maybe, have the Earth explode as the game is finishing but him landing on a Combine planet and let him free them too. Okay, just joking but something new is definitely needed.
Maybe the question should have been “who would you least like to die?”.