So Harrison,

Which Aliens comics did you check out?

As for the Indiana Jones and the Fate of Atlantis comic, I didn't like the story in it as much as playing the actual game, plus it really didn't need alien beings to explain the Atlantians' level of technology or the whole mutant war.

Yes, Dark Horse did many movie tie ins but I can't say it was always good stuff, some franchises are really difficult to write comic spin offs for and Dark Horse seems to pick up all the action movies.