I'm never sure which albums the general Fates Warning fan bases likes/doesn't like. I think it's because people's opinions are all over the place. But I've gotten the impression that both Disconnected and FWX aren't as high on fans rankings as they are on mine. FWX is a really good album.
For whatever reason, both Disconnected and FWX fell flat for me. There are only a small handful of songs on the two that ever resonated for me.
Since you mentioned rankings:
APSOG: Not just FW's best album, but a top 5 all time album
Perfect Symmetry: The first "new" FW album for me. I was absolutely blown away by the opening track, Part of the Machine. As a whole, it's prog metal masterpiece, with the only instrumental I would put on the same level as La Villa Strangiato. The only weaknesses are, surprisingly, two of the Frank Aresti songs (A World Apart and The Arena).
Parallels: An almost perfect blend of prog and accessible metal. It's what Queensryche tried to do with Empire, which is, for me, an ultimately disappointing album. But FW nailed it.
DIADL: Given my disappointment with Disconnected and FWX, I was cautiously optimistic when this album was announced. Songs like I Am and Into the Black kick serious ass. They're better than the two "lead" tracks, One Thousand Fires and Firefly. But the hidden gem is And Yet It Moves. It's a song that fits its title to a T. From the intro to the end, it never fails to impress. Quite possible FW's best single song ever. An honorable mention to Falling Further on the limited edition bonus disc. It's a song that would have fit proudly on Parallels or Inside Out.
No Exit: A little while after Operation: Mindcrime came out, I saw something on MTV saying, "if you like Mindcrime, check out these bands." They mentioned Dream Theater, Fates Warning and Crimson Glory. I went hunting and couldn't find anything by Dream Theater, but I found No Exit. I was a fan immediately. Side 1 sounded like a slightly heavier and less polished Queensryche, but The Ivory Gate of Dreams on side 2 was on a completely different level, from the acoustic intro to the harmony guitars on Quietus to the gentle Whispers on the Wind, to blistering conclusion in Acquiescence and its epic ending.
Inside Out: If there had been no Parallels, this album would have gotten a lot more run, and I honestly can't figure out why it didn't keep up the momentum FW had gained with Parallels. There are a couple clunkers, but it's strong from start to finish, and Monument is a great song.
The Spectre Within: It's a bit unfair to compare the Arch albums to the Alder albums. For me, Arch's voice is ok, but I don't like a lot of his phrasings. Awaken the Guardian tends to get more run than Spectre, but I like Spectre a little better. The opening track, Traveler in Time, is probably my favorite Arch era song, and The Apparition and Epitaph are also great.
Awaken the Guardian: The line between Guardian and Spectre is slim, and you could really tell here that good things were coming. Fata Morgana, Guardian, Giant's Lore and Exodus are the standout tracks.
Theories of Flight: This album hasn't quite connected with me yet. It's much more moody and atmospheric, like Disconnected and FWX.
Disconnected: As mentioned above, only a few songs on this album and FWX have connected with me. I like Pieces of Me and Still Remains.
FWX: Another Perfect Day is a bit of an outlier on this album, but it's the only song that ever really connected for me. Some of it has to do with what was going on in my life when this album was released.
Night on Brocken: This album is very much analogous to Rush's debut. Very derivative, raw and immature, but still showing signs of brilliance to come. Damnation is the standout track.