Because Gordon Freeman is the archtypical scientist.
I think you need to press for some feature that makes these characters more original, memorable, as well as to define them more clearly in the roles you've set. For instance, I don't think you have to push the skull thing so much, because people actually want to see skulls everywhere and nobody who isn't comically evil would make a robot that is an evil cowled skeleton deliberately - but you can suggest it with skull-like features, people will still get it. Basically, you can make it a lot more robot-like and the skull thing would still work, plus the character would be visually distinct from other characters that are basically skeletons.
The scientist should look more like a scientist and less like every other action hero. Which doesn't mean you need to soften him up, just make him not look like (arnie/val kilmer/duke nukem/that dude from wolfenstein). Make him scruffy or play the arctic thing to its extreme, or stick the goggles on him and fancy them up, or just add unique accents to his clothing or even just change his hair. Even just a big nose would do it. Just do something that makes him not that same chiseled crewcut good guy, again.
