tl;dr - Sunblade writes too many words about Final Fantasy again
If I was gonna rank and analyze the FFs into how well they use their dungeons, I'd split them into 2D and 3D. Then they'd go something like
2d: V > III > VI > IV > I > II
3d: XII > X > VIII = IX > VII* > XIII
I: Pretty run of the mill as far as dungeon design goes, which is a given since it came first. Has a the diverse spread of earth/fire/water/air locales and the layouts are standard multi-floor / gotta find the stairs to the next floor afairs, with the Sea Shrine prob being my favorite of the bunch by playing with the floor numbers. Nothing too impressive visually, since most dungeons reuse the same cave / ruins tileset.
II: Fuck the day Kawazu decided to implement pointless, empty rooms in every single dungeon in the game.
III: Probably the most creative of all the 2D games. Lots of interesting gimmick dungeons, multi-floor dungeons with varying conditions to keep climbing, as well as interesting locations. The two major things that drag this one down are an overreliance on Mini dungeons (we get it, you like your status effects) and, as cool as they are visually, the marathon trek that is Labyrinth of Ancients > Crystal Tower > World of Darkness without being able to exit in between.
IV: Pretty zzzzzzzzz to be honest. The highlight of the game is going inside a robot, otherwise most of the dungeons are straight point A to Point B affairs with branches for loot. The Underworld section is notoriously bad too, since it starts adding in labyrinth dungeons with damaging floor tiles that force you to recast Float every single time to move up or down a floor (and god forbid you haven't learned Float yet). The Lunar Subterrane is prob the most complex dungeon in the game, which isn't a very high bar.
V: Stands out the most among the 2D games. Lots of interesting and varied locales, FF5 manages to make every dungeon feel significant, unique and not filler added to pad out the game. Drakenvale feels nothing like Mt Karnak, despite both being mountains. The Fire Ship's layout is really unique as far as FF dungeons go. There's interesting gimmick dungeons like the Pyramid and Fork Tower's Physical / Magic split. It even has FF4's damage floor tiles exclusively for one dungeon, but not nearly as annoying because there's more ways to circumvent the damage. FF5 is by far the biggest standout when it comes to dungeons.
VI: While sporting some of the most complex dungeons in the 2D games, VI suffers a lot from its dungeons being straight up
not very interesting. For every Phantom Train and Magitek Research Facility, there's three Caves, Castles and Mountains. I only recently played it to completion for the first time like 3 years ago and damn if I can remember 90% of its dungeons. I get
why its designed that way, specially during its second half, but I don't have to agree with the design choice!
VII: This one is weird to analyze. VII plays a lot with the idea of just what a typical "dungeon" is, since most of them are accessed through towns, some exist during temporary moments (such as the Sector 1/5 Reacots), and some have sections, like parts of the Shinra Headquarters raid, where there's zero combat involved, or totally open areas like Corel Prison. Hell, you could go so far as to consider areas like the Wall Market as pseudo dungeons where you spend a long time trying to puzzle out how to "clear" the section. Really off-beat game.
VIII & IX: I lump these two together because I've played neither recently enough for me to make good judgement calls about the quality of the games. I do remember some neat locations lke the final dungeon in VIII and Ipsen Castle in IX, but that's about it.
X: First one to actually try to have semi-complex dungeons like the 2D games. Helped a lot by introducing a minimap to help out with navigation. Pretty decent overall, with the Cloisters of Trials generally standing out.
XI: Zero interest in playing these days.
XII: woah its a 3D ff with large expansive dungeons, really creative gimmick ones, dungeons where you're given an incentive to return to them at multiple points in the game, and even optional dungeons that exist purely for exploration's sake and not to drive the story forward. There's a lot to love about the dungeons in XII that, despite some stinkers like the Giruvegan crystal, a vast majority of the dungeons in XII are pretty unique and try to do different things within the game, my personal favorite being the entirety of the Pharos, which is tehnically composed of like three different dungeons.
XIII:
(Image removed from quote.)
XIV: Not included in the rankings cause it goes for different priorities than your normal single player dungeon. The actual layouts are generally Point A to Point B hallways, but the visual spectacle and themes for all the dungeons are generally really on-point and never fail to deliver in that regard. It's all about the boss fights here anyway.
I can't really compare the dungeons across SE RPGs cause I'm not too savvy about them, but if I could, I'd put Chrono Trigger's to be just as good or better than V's.