I totally agree. Aliens is a piece of cinematic history. But it's the thematic differences that ultimately seperate the two for my personal taste. Cameron made a film that Cameron does best; an action adventure with a cast of clearly defined (if simple) characters, ripe with one liners and very memorable set pieces. He did something that was a polar opposite to Alien, turning the action and presentation dial to 11, and creating one of the most memorable action horror films ever made. It's absolutely excellent and I don't deny that.
But it's his thematic choices that makes it a lesser film than Alien for me personally. I much, much prefer the slower, brooding tension and horror of Alien, the less 'cinematic', punchy cinematography, the drawn out pacing, and the far, far more natural flowing dialogue.
Ultimately nearly everything I love about the series came from Scott, not Cameron. I liked his portrayal of the xenomorph much more. I preferred his characterisation of Ripley. I loved the horror, and the overall atmosphere surrounding LV-426.
I feel Aliens sticks in peoples minds more because it's a better mass market action film. Its a summer blockbuster, and a very, very good one. Similar to Terminator, it has that iconic Cameron touch to the presentation and adventure that you just cant ignore. But for me, Alien will always be the film Alien, and Cameron's work, as good as it might be, a lesser experience.