Going through a list of all Pokemon, and stopping when one strikes me as less well known:
The Mankey line has abysmal distribution, being found normally only in Kanto and one Johto route. Anyone playing casually probably hasn't seen one since HGSS/FRLG.
Seadra has been reduced to near irrelevance by Kingdra.
Ledyba is a classical shitmon with mediocre distribution, though its uselessness is somewhat memorable in itself.
For a Pokemon in almost every game since its creation, Chinchou is remarkably unremarkable.
Hoppip's distribution is also surprisingly poor, though its ubiquity G/S offsets that a little.
Girafarig is underutilized, though memorable.
Honestly, who has any reason to think of the Snubbull line on a regular basis?
Teddiursa's line is another Gen II obscurity, along with Corsola, Phanpy, Stantler, and Smoochum.
Masquerain is only remembered for ruining a novel typing.
Torkoal, Spheal, Clamperl, and Relicanth round off Gen III.
Kriketot is pretty forgettable.
Burmy, Buizel, Cherubi, Shellos too. Lots of Gen IV gimmick-mon.
Happiny is particularly irrelevant among its irrelevant peers.
You'd be forgiven for thinking Lucario is a basic Pokemon, considering its prevo is Riolu.
Carnivine is just an oddball.
Lumineon is probably the most memorably unmemorable of them all.
Mantyke, most of the Rotom forms, Shaymin (since it's an event-only legendary that will never get another proper event).
Tympole, Maractus, Minccino, Heatmor. Gen V, against all odds, did a good job showcasing its 150+ mons.
Vivillion's prevos receive none of the attention Vivillion itself receives.
I'm sure lots of people willfully forget Spritzee and Swirlix.
Binacle and Bergmite are a bit out there.
