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Probably...
1) Totodile - I just love it! It's so cute! Croconaw looks a bit, ugly, which makes it worse. At least Feraligatr looks and fights like a total BAMF to make up for that. If it weren't for that, I'd never evolve Totodile.
2) Any Pokemon that doesn't learn any moves after evolving (i.e. Clefairy --> Clefable)
3) Trapinch - Vibrava's got a double ice weakness, unlike Trapinch. While that's not inherently bad, it makes Vibrava much harder to train/use, especially in a Nuzlocke run, because it's stuck as a Vibrava for freaking ever before it evolves, and Vibrava can't take a hit from an ice attack, while Flygon might, and can hit hard and fast to prevent the attack from coming.