A couple I thought of are volbeat and illumise. I remember scourging Hoenn for an illumise after I first saw one and thought it was adorable - they're a very uncommon sight in Sapphire version. And volbeat started to grow on me with its amusing, albeit annoying battle antics (confuse ray + double team + moonlight = a hair-pullingly long battle). Plus, they're a pretty cute greaser/flapper couple. It seems few others remember them, and the few times I've heard them mentioned, not much good was said of them. I guess that's what happens when you're non-evolving members of one of the most unpopular types out there.
It seems pretty hard to get recognition as a bug-type, as they're usually pretty niche in terms of general appeal factor, not being all that popularly seen as cute or cool, and a lot of them lacking any battle effectiveness to make up for it. Another bug I like which not a lot of people do is wormadam - like volbeat and illumise, if I've heard someone else mention them at all, they usually have nothing good to say about them, and yeah, it doesn't do much in battle, and sure it isn't even the first or best bagworm (though forretress is lucky to have got a key role in a lot of the metagame, I bet no one would ever remember it otherwise) but it's got one of the most melodious voices in gen 4. Also, the steel-type one is floofy. At least it's just a tad more memorable than mothim, who's stuck basically being a throwaway hybrid of wurmple's final forms (which themselves have a hard time keeping out of the shadow of butterfree and venomoth).
Spinda's another one of my gen 3 favourites that doesn't get much recognition, though I think that's to a lesser extent than the fireflies, seeing as at least they've got their spot thing and a pretty memorable route all to themselves in Hoenn.
Also, I'm probably the only person whose favourite dog pokémon is snubbull. It and houndour's line were the only real dog pokémon in the Japanese-based games - most of the other ones were semi-shishi/wolf/fox thingies which seemed to get more love from dog lovers than the true-blue pupper, snubbull. And getting to be fairy type barely did anything for it by gen 6, by which it had plenty of other dog pokémon to overshadow it (including a rival fairy-type dog in slurpuff). I guess ugly-cute is a hard sell for a lot of people. At least with its being featured in Pikachu's Vacation, it's a little less forgotten than granbull
That and also for how Seel looks far too similar to an actual seal with the only difference being Seel has a horn, how Seel and Dewgong’s shinies barely change, and in Dewgong’s case there are much more useful Ice and Water types than it.
I actually think seel's design is underrated - it's a pretty clever, yet natural blend of seal pup (body/fur colour), walrus (tusks), puppy (snout/tongue) and narwhal (horn). I think people mainly knee-jerk dismiss it as unimaginative due to its having pretty much THE most unoriginal [English] name of any pokémon. Well, that and its never getting anything new as dewgong, besides having most of its more interesting features reduced and leaving it looking even more like just a straight seal.
You're right, and it's even weirder when you consider that Iris owned a Doryuzu (Excadrill) in the anime, yet that doesn't seem to have made the species popular with the fandom.
Excadrill seemed pretty memorable in the competitive scene, at least, being strong enough to be one of the few non-legendaries to be considered uber.
I would argue the Gen 2 starters - particularly the final forms - don't get near as much love or recognition despite being my favorite starter trio. My guess is because a lot of the other gens have gone out of their way to give their starters secondary typing or other forms of competitive viability.
Can't argue with that - and not only do none of them have distinguishing secondary types, they always get passed up in terms of getting new forms. Though I guess the gen 3 starters may have been purely lucky that it happened to be gen 3's turn for remakes by the time megas were being come up with.