Why is always humans the bad guys, why can't can't they be dwarves or elves?

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From what I gather, you haven't read Universal Acceptence. I don't normally make a story like this because of the simple reason most people don't like it when humans are the 'bad guys'. Even if the story had a more dwarven or elvish feel to it, the closest way for people to feel empathy for certain characters is to make said races with a human-like mindset. Otherwise, the reader wouldn't understand for the majority reason what's going on.

(I will give this hint about Universal Acceptance just to smooth things over.) In this particular story, their are actually multiple different 'humans'. It's also confirmed in Universal Acceptance as well. The protagonist is a different human than the masters were. So that's why the 'unnatural looking' humans are what Shadow noticed to separate them from the normal human beings he's seen on Earth.

If you want to know more about his multiverse travellings I put the links of the other two stories in the title description.

My goal in writing 'bad guy humans' is not to demonize humanity, but to show a bit of a different world with different rules. And a more not-black-and-white universe out of so many in fiction.

You might got that impression when Shadow saw the first in the Elite Master circle and got enraged, but his rage is more deeply rooted than shallow anger for no reason. And if that doesn't convince you then just know that all information about the 'unusal humans' haven't been revealed yet.

Edit: A little bit of an error, but fixed it.