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Mantine (gen 2)
I've already talked a bit about Mantine being a relatively obscure mon in general, but I'd really like to highlight how Gen 2's trend of making their own generation's mons unnecessarily rare also affected Mantine. In Johto, Mantine is only found in Gold, Crystal, and Heart Gold, needing to be traded for the Silver versions. It is only found in one singular route, that being Route 41. It's luckily a fair bit better than the 1% mons featured in this thread, being at a gracious 10% through Surfing!! The issue with this, is that by being on Route 41, you already have a mon that can use Surf, likely a Water type. And on top of that, you're probably so annoyed with the constant Tentacool encounters that you've blasted your Repel for the entire route as you make it to Cianwood. You'd have to be seriously lucky to find this thing on your first venture through Route 41, and it's available nowhere else in the game. As far as I know, I don't think any NPCs use Mantine either, at least in the original GSC. (It may have been changed in HGSS). So yeah, redundant Water type that's version-exclusive, in one route only, and is a bit rare on top of that. Johto's work at it's finest.
Mantine was done so dirty for so long. It's only catchable in one out of the five Gen III games - LeafGreen - and even then with a miserable appearance rate. Even though it gained a pre-evo in Gen IV and was lucky enough to make it into the DP Sinnoh Dex (though I believe every Pokemon with a new pre-evolution did; it's just most of the ones with forward-facing evolutions that missed out) it's pretty invisible in those games; not used by anyone in the Water-type gym and not given any prominence.
Then in B2W2 we're told that Marlon learned to jump out of the water by swimming with Mantine as a child, so it's one we're meant to associate with him. Fittingly, it's on his team in the anime, and in the games...
...it's only on his team in Challenge Mode.
USUM finally gave it a spotlight, but damn did it have to wait a long time to get it.