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Hmm, well first what do we considered underrated? With Pokemon there's several reasons why a Pokemon would be underrated (and these reasons can be stacked too):
1. It's a pre-evolution, especially middle. More attention is paid to the final evolutions of Pokemon than their pre-evolutions by players. Adding another layer to this, GF and Pokemon Company pays more attention to both the final evolutions and basic stages, resulting in many middle stages to look like a transitional stage, bigger version of the basic stage, or smaller version of the final evolution. Also Baby Pokemon generally are ignored, especially ones with an ugly simple design.
2. Lacks battling potential. There's two ways a Pokemon lack battling potential. One is just that it just wasn't given what it needed: low/misdistributed stats, useless/bad Abilities, and/or shallow movepool. The other is that it has what it needs, but there's other Pokemon that does what it does better.
3. Unappealing design. Everyone has different tastes, so all sorts of designs are used for making Pokemon. Some stick, some don't.
Now with that established, where to start? I know, how about the Gen I Starters!
"The Starters... the most popular and beloved of the Starters if not of all Pokemon?"
Yup, nostalgia beside even they succumb to this:
Gen I:
Ivysaur & Wartortle: By the way, get used to me mentioning the middle stages. Cases of number 1, which is sad as I think they look pretty nice. Ivysaur you can say is a bigger Bulbasaur, but I feel what they did with the plant on its back sprouting makes up for animal part of it not changing much. Wartortle has an eye-catching design with the furry ears and tail its other evolution family lacks giving it a look all its own. "Say, where's Charmeleon"? Eh, you can call me bias, but due to Charizard's popularity I think Charmeleon also gets elevated a bit so that's its not completely forgotten about (gotta get through it to get Charizard). Charmeleon has that transitional thing going on, it looks like an older Charmander with a more rigid face, grew a horn, and has protruding claws. But Charmeleon has its own uniqueness, being a bright red.
Venusaur: We've all heard the jokes: you pick the Charmander, your rival picks the Squirtle, and Bulbasaur is left to rot. Or you picked the Squirtle and your rival picked the Bulbasaur, forever destined to lose to you. But that's no fault of Bulbasaur, but of Venusaur and case 3. Charmander becomes a dragon, Squirtle becomes a giant turtle with cannons on its back... and Bulbasaur just becomes a warty toad with a tree on its back. In addition its a startling jump, Ivysaur's animal part didn't change much from Bulbasaur so what it becomes as a Venusaur sort of comes outta left field. Sadly even its Mega Evolution suffers this, looking barely different except with more leaves and a flower on its head. But I don't dislike it, the design may be "ugly" but its a good & fierce looking ugly, I like they kept with the bulb growing idea with it becoming a full fledged tree/flower, and it certainly has its fans.
Mega Charizard Y: Course, at least for Mega Venusaur it's the only Mega Venusaur. Charizard popularity has given it two Mega Evolutions, one that becomes a black Charizard with blue flames, spikes, and a Dragon-type. Then the other is a stronger Charizard. Which is unfair, as MCY has the way better design than MCX plus is a pretty powerful Sunny Weather summoner. But it's a victim to case 2, MCX is just considered better probably due to it losing its Flying-type (losing that quad weakness to Stealth Rock) and gaining a type that's both defensive and comes with powerful moves it gets STAB to now. Also a black Charizard with blue flames looks cool. Kind of wish they had a Mega Charizard Z that combined the design of Y with the colors of X, not sure what the stats and Ability would be though.
