Some of the older ones I kinda wish made a comeback, as I feel some of New Leaf's puns... well, they just kinda used their best ideas early.
"I caught a squid! Oh no I squidn't!" ~ Wild World "I caught a koi! Don't be coy! (Ugh.)" ~ Wild World "I caught a bass! If I can catch a drummer, maybe I'll form a band!" ~ GameCube "I caught a bluegill! Don't worry, I caught the rest of the fish, too!" ~ GameCube
That, and I particularly like the whole dab/olive flounder confusion too.
"I caught a dab! Oh wait... are you an olive flounder? Oh, yeah, you are, aren't you?" ~ Wild World "I caught a dab! Didja see it? ... You're a dab, right?" ~ Wild World
( thankfully, this joke came back in New Leaf c: )
"I caught a shark! GAH! Why am I holding it?!"
"WHOA! I caught a golden stag! Better not spend it all in one place!"
"I caught a sea bass! What?! You again?"