Best Boss Ever: The final boss fight, a team fight against DraculaandDeath at the same time. For many games, you're told that Death is Dracula's right-hand man; here, you see it for yourself why.
Evil Is Sexy: Stella whose dress sports Absolute Cleavage that bares her head-sized breasts. And she turns out to be a subversion, as she still wears that even when she's good.
Fridge Horror / Tear Jerker: The Circus of Fear. It's mentioned that Brauner lost his daughters because of the first World War. The painting (and by extension, the stage) shows the aftermath of a circus and town torn apart by war. Put two and two together. Worse, as you go further into the level, the stage gets turned on its side, and then upside down, representing how Brauner's life was literally turned upside down. And then there's the boss...
Game Breaker: Sisters mode is incredibly easy for two reasons: the sisters float and hover in the air (at the cost of MP), and their method of attack is entirely done by the touchscreen. Stella does physical attacks by rubbing the stylus over, while Loretta launches a barrage of ice magic where the stylus is placed. With Loretta, even ice-resistant enemies fall in seconds (save for mage-type enemies). Attacking also consumes MP, but on the ground they recover it quickly. They're also immune to all status ailments. Of course, you have to beat the game just to unlock the mode to play as the sisters first, so there's not much of the game left to break.
Charlotte can learn a spell called Ice Needles that is bought early on in the game. Because of its fast cast rate, multiple "needles", low mana cost, and high damage, it's incredibly useful for taking out rooms of enemies with ease, even late into the game. Later in the game, Chain Lightning can be gained, doing huge damage to every enemy onscreen when fully charged.
Similar to the Charlotte example above, Jonathan can buy the Shuriken subweapon really early in the game, and you'll almost never need another one. It's easy to master, and when mastered it basically obliterates anything in front of or below you.
The fully powered Vampire Killer, while not the strongest weapon by any stretch, is ridiculously good due to the typical speed and range of the whip combined with a high enough attack power and holy/flame elemental, especially when the special attack is used. This does huge damage to many enemies. Other, stronger weapons are often much slower and their specials aren't as good.
The Cross subweapon, which can be obtained from a quest unlocked somewhere between halfway and two-thirds through the game, is flat out ridiculous. It does solid damage, penetrates enemies, can score multiple hits against pretty much anything with good aim, can strike enemies behind you as well if you jump out of the way when it comes back, and has an elemental advantage over virtually every creature in the game. It doesn't cost all too much MP, has good reach and an easily predictable flight pattern, and becomes downright HUGE when mastered, which also lets you throw two of them. In other words, it's pretty much a Boomerang, Bible, and Shuriken compressed into one highly potent package. Not only does it make clearing rooms a snap, but it also flattens all but a couple of bosses (most of which show up BEFORE you can obtain it), but it also makes the optional level restriction runs incredibly easy.
The Sage Ring boosts mana regeneration; when you have two and Charlotte's Healing spell, you have FREE healing (if you are patient). A similar thing happens if you equip healing mail and walk against a wall.
Good Bad Bugs: You can duplicate quest rewards for early access to the Holy Claymore. You can also glitch the vampire sisters with a deft usage of Clear Skies, freezing them in place for the entire remainder of the battle.
Hilarious in Hindsight: The main pair make an impressive team. Jonathan is the truly talented one, with the training necessary to accomplish his goal, but he suffers from deep self-esteem issues. The younger 16-year-old Charlotte accompanies him with her own (even if considered lesser) talents and much-needed moral support, allowing him to reach his full potential. Cue the sixth season of Britain's Got Talent and the second-place team of opera singers Jonathan and Charlotte, who have the exact same team dynamic.
The skill mastery system in general. For starters, Charlotte cannot help you master anything, even though you'll be using her for about half the game. And Jonathan's just take forever to master. Almost every skill has a SP requirement in the thousands, and you get one or two from almost all monsters. You get SP as long as the monster has been A) damaged by the skill, and B) the monster dies by your hand, which is simple enough. The other big problem is the damage of the skills, since their power comes from the INT stat which Jonathan just doesn't get naturally. It is perfectly possible to finish the game without mastering a single skill (or even realize there is such a system in the first place), using Charlotte sensibly and the few skills that are mechanically broken (Cross, Bible...).
One of Wind's quests requires mastering the Cross, Bible, and Holy Water. According to Pink Kitty Rose, the most efficient way she found to master all these was nearly two hours of non-stop minotaur farming.
Sisters mode is unplayable if you're left-handed. You use the touchscreen to attack and the D-pad to move, which basically means you must "draw" your attacks with your right hand. And no, you can't reassign the controls so that you can move using the face buttons.
You can just try to survive against the Creatures for sixty seconds, at which point the door to the next room will open whether they're beaten or not. Not that this is much easier, mind.
And you can forget trying to beat these two if you're playing with any of the alternate characters.
The purification of Stella and Loretta, where casting Sanctuary takes 15 seconds and Charlotte cannot get hit during it or it fails, nor can she go offscreen, and if either character gets hit, that's like a 3KO, and it's even worse on Hard mode. Trying to do this at low levels can make it pretty much a Luck-Based Mission. Stonewall is your friend here.
Worse? Sanctuary has a range of one screen-width with Charlotte as the center. Since you'll be playing as Jonathan keeping the sisters to one side so Charlotte doesn't get hit, it's possible for the spell to miss.
One saving grace is that you only need to hit one of the sisters with it for it to work.
Death can also have shades of this, being Death and all. He has several attacks that are hard to dodge even if you know what you're doing and can kill even prepared players with ease.
They Wasted a Perfectly Good Plot: Brauner believes Stella and Loretta are his daughters reincarnated, but this is never explored and we don't get any confirmation for one way or the other.
Of course, it might've just been put in to show how insane he is.
There's an Axe Armor mode, but no John Morris/Eric Lecarde mode, despite this game being a sequel to theirs. And/or even a Castlevania III: Dracula's Curse mode, since the sprites for the player characters in that game (except for Alucard) are in this game but used for bosses (recycled from Symphony of the Night).
Unwinnable by Insanity: It's possible to render the Nest of Evil completely unescapable by not triggering the teleporter next to the entrance and then going all the way from the first floor to the bottom floor in one go and using the save point at the bottom.