Logic, mostly. The game's planned resolution is 320x240. Have you ever even seen, much less used a monitor that small? Even if you have, such a monitor would be vanishingly rare today. There's no point in evaluating the sprite at 100%; It will never be seen at that size ingame.

When you're working with a SNES-like resolution you basically have to make every thing read correctly at 200% zoom, and there are certain things you can't get away with at 200%. Certain details become noise, you may end up resorting to a massive palette, etc.

While unintentionally shortening everything above the eyebrows might make a Loomis figure odd, it could be fitting for a caveman-character and clearly underlines that he won't have a lot of intelligence (just sayin)
Same goes for the eyes - drawing bigger eyes can lead to another impression of a character than having small eyes - just considering why most anime styles tend to have huge eyes and no noses.

It's something I struggled a lot with, but limiting yourself on the "right" proportions which are "idealized" can definitely lead to very boring and exchangable cast of characters with very less overall diversity - it just makes one archetype so to say, while for character design diversity is key.

I prefer fantastical or stylized anatomies even when the subjects are rendered realistically. And I mean stylized expressively, not just empty tweaks. Frazetta's was great at that specifically. And while I'm yapping (woot tangent), why do so many artists create generically beautiful women? There are idiosyncracies in every person's tastes, after all. It's the same generic beauty shopping mall mannequins have.

Broadly speaking, discipline is obviously a good thing. But turning oneself into a human camera is a great way to sterilize your art. People will be impressed, sure, but they won't care . And that's what ultimately matters, I think. Obviously this doesn't apply to every field. If you're doing conceptual art for Boeing or something, by all means, be as technically precise as possible.

If it isn't literally Gordon Freeman, I'd change the face. I second the shoulder/arm comments as well.

progress

third iteration, beta

Edit:

Cleaning up