I was gonna say magikarp but since several people already said it, I'm gonna say manaphy. It's super weak, forever a baby Pokémon and somehow it's a legendary. Wtf why would they add this trash anyway? It can lay eggs that hatch into phiones which are somehow even more useless. I've never seen a manaphy used in battle ever.
I thought Manaphy had quite a solid niche with access to Tail Glow, high SpA and a decent Special move pool — The whole Phione thing is, I suppose, GF trying out a weird gimmick which they've yet to pick up again.
Unown, on the other hand, cannot even learn a single TM!! GF have poured so much effort into its lore, yet they've never really gone anywhere with it. Seemed like Sigilyph could have been adapted from an Unown evolution concept or something, but nope! Progress unknown in the Unown department.
Other than Unown, I'd say the BABY POKEMON all fall into the bracket of being useless — Phione would get bundled up in here as well. Split branch evolutions? Yes please! Single stage mons? Sure, why not! Baby evolutions? Please GF, don't do it again!!