Alternate Character Interpretation: The entire series is an Evil Plan by the Bunyips to get TY powerful enough to wipe out the Quinkan, leaving no force powerful enough to stop the Bunyips. Hey, they're not good guys in Aussie folklore, so their benevolence in-game is more than a little off-putting.
Anti-Climax Boss: In the second game, Boss Cass' final form is...Boss Cass himself. No fancy mechs (on his part), no special effects, just the one cassowary. Though hitting him with the Shadow Bunyip's Frickin' Laser Beams is a guilty pleasure...
The giant roaches can give those spiders a good run for their money.
For this troper, it was the mission in the second game involving crocodiles in the sewers. The 90-degree corners meant you could round a bend and just encounter a croc with zero warning. This is why I often saved the mission for last.
Sidetracked by the Gold Saucer: Kart racing! It can either be done from the main story mode (where it's theoretically a useful way to get opals, but we know you're just doing it for fun) or as an option from the main menu (so you can skip the middleman, play any character you want, and even go on a grand tour of all the courses in the game).
Stop Helping Me!: A literal case for Lenny the lyrebird. However, he's not as helpful as you'd want... until you start doing the opposite of what he says. He later gets a job telling stories to kids in daycare, which are actually all true, being recountings of boss fights from the first game.
The Scrappy: Shazza, Lenny the Lyrebird, the frill lizard and goobo in charge of the Bush Rescue Training Program in 2 and Dennis.
They Changed It, Now It Sucks: The voice acting changing between games one, two, and three, and the excess of mech or Gunyip levels in game three.