It's all subjective, obviously, but ATLiens is number 1 for me. I like dustier production in general and I love Elevators. I remember when that shit came out and it's like being enveloped into a cloud of smoke. Nothing else feels like that song. The title track epitomizes Outkast to me in general.
Aquemini is great, because it showed an interesting evolution in what they were doing; expanding their sound and identity, as opposed to all out abandoning it. I remember seeing the Rosa Parks and Skew It On The Bar-B videos on Rap City back in the day and they were both instantly engaging and stand out cuts at the time. That title track is amazing, too. You knew they were doing something and could, arguably, make it a better overall album, but personal connections and context are difficult things to separate or account for.
I'm not trashing Stankonia, at all, but The Rolling Stone list is clearly made by people who are prioritizing the commercial hits and/or breakout albums, made clear by their reasoning, beyond the placements. Personally, I'd be good with never hearing Ms. Jackson ever again the way that was beat into the ground and that's the major selling point for them. I just don't think it's the second greatest hip hop album of all time.