They are such different games.
In Jaws I feel like there's always many things going on, meaning, you have a higher chance of hitting a shot that does something for you. I think that's because it's constantly throwing different modes at you. Alien feels much more focused, you start a mode by hitting 3 shots, and then you have to hit the shots for that mode to be successful. Yes, there's other aspects, like adding an MB or using weapons, but it feels more linear to me. The rules kind of play more like a WMS game, while Jaws plays like other modern Sterns.
When it comes to the theme integration, and the use of movie assets, I think Alien wins out no question. Jaws just feels like chaos to me with the constant switching between video clips that are completely unrelated (this goes back to my comments about the rules). I think Alien is the best total package, but gameplay is going to be completely subjective to your preferences. If you can play both, definitely do that first.
I had Alien on order before Jaws was revealed, because I knew I'd appreciate the theme better. I'm happy I have it over Jaws, personally. I'm also not a huge fan of modern Sterns (own 0, but do play them on location to chase local IC scores).
Also, compare the differences in the LV and RV models. You might find you like the RV more and can save some $$$. I've detailed those here for someone else in a previous post.