Game-Breaker: The Item Duplication Glitch. It's a method that allows you to create up to 99 of any usable item. To which you can duplicate stat upgrade items, alignment upgrade items, even Champion Statuettes!
Ho Yay: Any scene featuring Yumil and Magnus is full of this. Like Yumil asking Magnus to "become his knight".
Grapplers, as they hit hard no matter where in the formation they are, and always come in groups of 3 or 4. Thankfully you only face them in a few levels and you can get one.
Faeries and Gremlins, as they're Fragile Speedster incarnate and will dodge your attacks half the time. They only get real bad when paired with a healer at least.
"Harassment Specialist" units tend to be this way: squads containing lots of status and debuff-casters like the above-mentioned gremlins, fairies and also witches. They're typically not dangerous in terms of damage but since they can put your soldiers to sleep, paralyze them or just decrease their attack power, they can often hold off superior forces (and when you consider that 'losing' a battle, even on technicality causes your unit to retreat back a ways, it can cause a lot of issues).
Cockatrices can petrify you and the cure for that is not cheap. Also, on your side it robs you of experience as petrified enemies don't give any. At least you can upgrade your Golems into Stone Golems thanks to them.
While the special character Meredia is intended to join at level 17, a glitch enables players to get her as low as level 3, allowing them to abuse stat-increase-upon-level-up items to shoot her INT up to ridiculous heights. If Meredia's trained this way, she can OHKO entire enemy groups by herself, possibly making her the most powerful unit in the game (at least when it comes to most damage done with a single attack) without using the Item Duplication Glitch.
It's Easy, So It Sucks!: Not really "sucks," since many fans of the game love the amount of depth that can go into character customization and army management, and also like the battle system, music, and story. However, the enemy group design is very poor and never improves, so as the player gets access to better classes and weapons, the game becomes less and less challenging. It can be a bit of a letdown that your well-trained death army never truly gets a Worthy Opponent.
Magnificent Bastard: The Glendale brothers, but Baldwin tends to be more bastard and Richard is more magnificent.
Scrappy Mechanic: Chaos Frame and alignment, two linked traits. While CF is supposed to demonstrate the difference between responsible and vicious tactics, it's so obscure that virtually all players fail to realize the difference between "capturing" a town and "liberating" it is anything more than flavor text. Alignment, while actual visible to the player is absurdly difficult to control in any meaningful as well.
Strawman Has a Point: A number of characters, even Rhade despite his Jerkass personality, bring up that rebelling against the puppet government in Palatinus will only bring about war with Lodis, which they argue is hopeless. Much as the player would hate to admit it, since this is also brought up by someone from the rebellion that sides with characters using demons, they have a point and no matter what ending you get, there's mention that will be a war with Lodis.
The Woobie: Mari. A common girl chosen to be the servant to Prince Yumil and falls in love with him... then loses Yumil, gets mind controlled, realizes her love for Yumil was artificially given to her by outside sources, accidentally releases a potential world-destroying goddess, and finally gets unceremoniously killed by Baldwin. Just when it seems like her existence couldn't be any worse, the low Chaos Frame ending shows that her child from Yumil is actually the reincarnation of Rashidi, meaning she's partly responsible for giving the Anti Christ godlike power.
In the latter half of the game, Prince Yumil. Having a crappy childhood and getting force-fed a fruit that makes you evil means that it's hard not to feel sorry for him even as he's killing people and trying to take over the world.