Musashi: Samurai Legend/YMMV

Nightmare Fuel: The modifications Malbec gave Arachnolia are terrifying, to say the least.
Ass Pull - Gandrake's motivation behind his villainy. Actually, that entire scene is one big Ass Pull.
- Not that much: apparently he's been controlled by a destructive goddess called Amestris (sealed in the Archnembulus) and manipulated. The fact that most of the information regarding her is almost cut out, though, adds to the confusion.
Complete Monster - Shiraz. He even confesses to killing his own colleagues within the company when ordered to, and he really enjoys his job. Plus he says he'll eat Musashi if Musashi doesn't defeat him.

Musashi: ...You actually enjoy it. You sadistic, soulless, subhuman...
Shiraz: Thank you. You're too kind.

Demonic Spiders - The red Ninjaroids, especially on the final level. But you'd better get used to them, as they're the focus of one of the few decent Level Grinding spots in the game.
- Also some late-level foes like the Vapor Knights.
Narm - Not that big an offender, really, but it does have some overdramatic quotes. Especially in the scenes surrounding Mycella's death.
Sequelitis - But then, Brave Fencer Musashi was a pretty tough act to follow.
- It's just a bunch of little things that made the sequel worse. A few more months of polish and a different voice actor for the new Musashi (in the western release) would have worked wonders.
- It was decent, and most of us weren't expecting a sequel to BFM, pretty much leaving Threads of Fate being a Spiritual Sequel until this one was released. Also, it kept the awesome music aspect.
That One Boss - Moltan, Arachnoblia, Asura and Nebulite Gandrake. Each of these is tougher in the arena sidequest, which imposes strict time limits. For some, it's best just to go level for a while and come back later.
Toy Ship: Possibly between Malbec and Mirabo/Maribo in The Stinger.
Unfortunate Implications - Subverted, actually, in most cases. While 80% of the plot consists of rescuing helpless, pretty girls, several of them turn out to be formidable in their own right. Istara becomes a friendly rival swordsman to Musashi, the Maidens of Fire (both of whom are small children) got captured by trying to calm an active, erupting volcano on their own, Fontina gives Musashi the information necessary to beat the second boss, and Princess Mycella even helps you in the final boss fight.