It's not so much goofy enemy design -- it's the whole goofy atmosphere of the rest of the game.
Look at DKC1 and 2. Yes, they had some goofy enemies, but the games still felt like they took themselves seriously. They weren't trying to be funny.
DKC3 and DK64 tried to hard to be funny -- and both completely failed at it.
I think the difference can be pretty well summarized by listening to the first level themes from DKC and DKC3.
DKC: http://www.youtube.com/watch?v=Bx7mI1rdykw "gorilla with massive testicles romping through the jungle. Everything in this jungle exists solely for him to swing on, climb on, or pound mercilessly." DKC followed this attitude throughout the game. While I wouldn't call the game "dark," per se, it at least takes itself seriously. It's not trying to be funny.
DKC3: http://www.youtube.com/watch?v=IOEU4a1IXMY "HEY KIDDIES! I'M GONNA HIT MYSELF IN THE FACE WITH A PIE! THEN MAYBE I'LL SLIP ON A BANANA!" It's like the fucking Jar-Jar Binx of the DKC trilogy.
Most of the game feels like this. Though there are select portions with darker music, the game overall feels like a little kid's birthday party. Also, after DKC1 and ESPECIALLY DKC2, this game was almost insultingly easy.
It had some decent level design and some creative mechanics, and was still fun to play, but the constant clown-like attempts at slapstick humor really pulled me out of the experience.