I’m going to totally cop-out here, and say that I like both movies equally, and for the same reasons. Sure, they are different movies, but there are several similarities, in my opinion:
Dedicated directors determined to bring a certain well-crafted vision to the screen.
Science-fiction that relies upon the empty vastness of space.
Special effects that were new and revolutionary at the time, and which still hold up.
The value, and sometimes worthlessness, of humanity - especially when pitted against nature and technology.
Mesmerizing designs and attention to detail.
Suspense.
Incidentally, since some of the best reviewed and received movies of all time had production problems and unintended results, Alien and 2001 are no exceptions. Cracked has several articles that discuss both Alien and 2001. If to be believed:
The quizzical and trippy portions of 2001 that everyone has questions about actually had narration behind it, sort of explaining what was going on and what you were seeing. I forget if Kubrick put it in, and the studio removed it right before release, or the other way around, but it supposedly exists…somewhere.
The screenwriter of Alien had some pornographic scenes written into Alien, I guess to stress the importance of biology and evolution with no regard to humans - like what we saw in Prometheus - and Ridley Scott had to do some serious rewritings to get around it.
Segue about the sequel, Aliens. Even if you are a die-hard fan who has seen it several times, I seriously suggest watching the director’s cut of it. It adds about a half hour that was cut due to time constraints. In it are scenes where Ripley, who comes out of space-sleep decades later, learns that her daughter, who was a toddler when she left, had recently died as an older lady. She missed her daughter’s entire life while she was sleeping.
Also, you see scenes of the colony on LV-426 before it was overtaken by the aliens, including the crashed spaceship that is explored in Alien. Very reminiscent of Uncle Owen and Aunt Beru on Tatooine before the stormtroopers arrived.
Also, you see the removed theatrical scene with the automated turrets running low on ammunition, as the aliens descended upon our space marines.
And, then, to tantalize or torture you further, Alien 3 was so bad because the budget and time was spent on so many different possibilities, including a well-received screenplay by William Gibson, that by the end, they had so little money left, they had to buy a cheap script, hire a then no-name director named David Fincher, and settle for a basic set, to film the movie that we eventually got.