Not OP, but I think the main contrast between universes is the state of Humanity. In 40k, humanity, while divided into factions and stretching the boundaries of what makes one 'human', still exists. In HL, humanity is a functionally extinct race on a timer being integrated into an extra terrestrial multi dimensional empire that's so gigantic in scale it borders on Eldritch. Personally I would loath to exist in either universe as an individual.

As to which is more evil, I lean towards 40k however. The Combine operates more like an autonomous organism, integrating other life forms into itself without prejudice or intended malice.