- Contested Sequel: From the reversion of the bombs to the grid-style of the classic games, to the altered level design and extended health bar by default, to even the more anime-like emphasis on character dialogue and story, the fandom is split between whether this game or its predecessor is the better title.
- Foe Yay: Bomberman and Regulus/Bulzeeb. Bulzeeb is very eager to settle the score with Bomberman, and even does The Only One Allowed to Defeat You schtick by saving him from Zoniha. Even the other Knights note how Bulzeeb gets excited whenever Bomberman is brought up. Then there's a comment about how he "makes his warrior's heart sing" in a cutscene if you clear Aquanet after Horizon. Bomberman also seems enthusiastic about having their eventual rematch in the good ending.
- Fridge Logic: Obviously this was done for the purposes of working with the gameplay and resulting story, but — it's kind of weird that Bomberman as a bomber wasn't able to utilize his ability at all without the Fire Stone on his person. Where does that leave the other bombers in this universe?
- Why is Neverland, a fire-and-steel-themed planet with no organic life to speak of, known as the "Nature" Planet?
- Scrappy Mechanic: It's an early 3D Bomberman game, so naturally the game tries to switch up the camera angles. The problem is that the controls don't really orient well for this, especially as the level design is still rather grid-focused. Judging how blocks may move or how your explosions might path is more than a bit problematic, and you have no camera control this time around which only further exacerbates the depth perception issue that Bomberman 64 had.
- The Scrappy: There's a number of reasons why fans aren't too torn up that the games after this one de-emphasized Pommy from a main character role to just being the basis of the Charabom system. Primarily, he's used to narrate just about everything for progression in place of Bomberman, but his Miles Gloriosus habits and constantly running into your bombs is bound to wear on the player's nerves. It was rather brazenly obvious that he and the Charaboms were added to Follow the Leader on the whole extensive Pokémon craze at the turn of the millennium, but it simply didn't work out.
- Suspiciously Similar Song: The first pre-boss theme sure sounds a lot like the James Bond theme...
YMMV / Bomberman 64: The Second Attack!