Anticlimax Boss: Chetyre. One wonders if the real Final Boss was actually Dragon-hybrid Bosch before it. Really, you can't actually lose against Chetyre, unless you don't realize you're supposed to push your D-ratio to 100%.
Capcom seems to (at least since 2007) semi-officially consider Dragon Quarter its Old Shame as far as the franchise goes — no promotional material has come out since a few months after its release in Japan; it is the sole game in the franchise never to have had derivative works licensed such as manga or drama albums; it is the sole game never to have had a port from its original system (Breath of Fire III did have a No Export for You PSP re-release and Breath of Fire IV did have a Windows port); and all new promotional material for the franchise as a whole (save a re-release of the Breath of Fire Complete Works artbook) has been for IV. This treatment likely is due to the badlyBroken Base outside of Japan.
Critical Dissonance: Critics generally enjoyed the game and gave it positive reviews. Fan reception, as noted above, was MUCH more mixed, albeit the game's reputation has improved over time.
Cult Classic: Despite the controversy the game has managed to win itself a small following of fans who consider it to be an amazing, tightly designed game that really doesn't deserve its backlash.
Ensemble Darkhorse: Zeno was beloved among the fanbase for her Dark Action Girl credentials, cool looking design, and completely awesome "Violet Death" skill linked to her sword.
Faux Symbolism: Most of the symbolism is from the Kabbalah, including a mockup of the sephirot in its official art with appropriate placements. Elyon's own name also fits in this imagery set. There's also extensive Christian imagery with several of the regents' names, the name of the org Trinity as well as some other hidden references.
Jerkass WoobieDestroyer Of Worlds: Yeah, Bosch's an entitled jerk, but anyone who's seen all his cutscenes knows this kid is severely messed up. A particularly disturbing SOL sequence shows Bosch killing a Genic five times his size at his father Vexacion's demand - before his voice broke.
That One Boss: The game is designed around the tension of the D-Counter and how it moves up, and so a lot of the game's bosses and even some of the regular enemies are very challenging specifically to tempt you to use it. Below are a few examples:
There's a boss gauntlet that happens after you get through the Ice Caverns; you are ambushed by Ryu's former boss Zeno, and then have to fight a grueling boss gauntlet. The first fight has you up against 8 soldiers (an extremely large amount that can very easily become overwhelming). The second has you fighting a Mighty Glacier of a machine that spawns smaller machines that can cast spells on you, and then finally the third one is a battle with Zeno herself and two more soldiers. Zeno is no pushover and can easily drain half of a complete life bar and more with her combos or just outright kill you if she has enough AP. She also becomes much more powerful upon getting close to dying, making her even more overwhelming. Getting through this entire gauntlet without using the Wyrm powers at least once requires a LOT of healing items and careful play.
The second fight with Bosch is the first to introduce a new mechanic that prevents you from simply damaging the boss as you please; Bosch will heal 1/4 of his HP at the end of every turn, meaning you need to outdamage his heals, something the player might not have an easy time doing without having the right abilities and equipment. It doesn't help that Bosch is quite vicious besides, being able to easily one-shot any of your party members should he go for the right combo. This makes coming into the fight with a multitude of healing items paramount as the fight can drag for a long time depending on how much you can damage Bosch per turn.
Vindicated by History: Downplayed. Reception to the game has warmed up a bit over the years, with people praising its oppressive atmosphere, small-scale plot, innovative New Game+ mechanic, memorable soundtrack, and challenging strategic gameplay. Some fans argue that the game was actually a work of genius and simply too ahead of its time.