Alien 3 went through lots of rewrites, although the overall product has a lot of merit. Resurrection would need edits when it comes to banter between the crew that Ripley aligns herself with. At least, Resurrection feels like it does needless humour.
By and large, the problem with the canon has been the inconsistent tone: each sequel feels different to the previous entry. Aliens is more cinematic than Alien, Alien 3 is without the gritty charisma of Aliens, and Resurrection is Alien 3 but to the extreme.
I'd say Aliens is the best because of the emotional story, and because of the momentum - aided by the dark blue palette, and dark sense of reality.
Alien does suspense well, and foreboding, but it's also too clinical.
Alien 3 is an odd case; on one level, it feels like a deeply relevant expression of existentialism, but on another is just downright gloomy.
In terms of tone vs. story, Aliens is impressive in having a harmony; it can technically be seen as not having a tone that suits the unrealistic nature of the story, but still works so very well because of the sheer excellence of details. Alien, meanwhile, has the more realistic story but suffers from too much emphasis on reality.