Both are incredible games. Great rules, great integration, etc. I think alien might have a slight edge on theme, Star Wars maybe a bit more solid rules. I own a Star Wars and would own an Alien if I could afford one.
Big problem with Alien is that the company isn't around anymore, and it has a lot of unique hardware. If it has issues you're taking a risk. If you can find a working one though and can take that risk, grab it! There aren't many chances to have one