Elemental Rock-Paper-Scissors: Brock thinks it's funny that some Trainers chose a Fire-type starter before coming to his Gym first (Both of Brock's Pokémon are dual-type Rock/Ground, both of which have type advantage over the Fire-type, which in short would make for a humiliating defeat to Red's Charmander). He's utterly humiliated when he finds out Charmander can learn Metal Claw.
Fake Difficulty: Lampshaded. The comic pretty much points out how cheap it is of the game to have an encounter with Blue right outside of Mt. Moon, meaning that the player's Pokémon are all weakened and unprepared for battle (meaning that they get their asses kicked).
Brock: You know, some people actually come here choosing FIRE as their starter Pokémon. Crazy, huh?
Only Sane Man: To some extent, Red is the human character who seems to make the most sense. Prof. Oak is forgetful, his assistant is a pedophile, Green is an Enfant Terrible, the Old Man is a geezer who complains about the term "evolution", Brock is creepy, the Team Rocket grunt tries to enforce his decrees by Pokémon battles, the pokémaniac is all too willing to battle someone who just untied him, and Red's Pokédex can't get over its juvenile sense of humor. About the only characters that have more sanity than Red are those two kids on Page 32 (see Level Grinding above).
The Power of Friendship: Red tries to forcefully capture Clefairy, but it escapes and looks sternly back at him. Can't blame a guy for trying... Clefairy shrugs it off and willingly captures itself afterward.
The Silent Bob: Subverted. Red may play this trope straight, but Word of God says that the addition of the Pokédex allows the main character to have a voice (even if it is one he very rarely agrees with).
Ungrateful Bastard: A mild example with the Super Nerd Red rescued from Team Rocket. He offered Red a fossil...only if Red battles him first. Naturally, Red tied him back up and made on his way. It helps that Red is very much an Audience Surrogate at this moment, as anyone who has played the games wanted to clock the guy in the jaw.