Before I really get into any sort of list, I'm going to get this one out of the way; I think Pikachu is underrated in an ironic sort of way. He's so ridiculously popular that he's unpopular for being overly popular. The only reason I ever see anybody give for not loving Pikachu is that Pikachu already gets too much love. So he's over-under-overrated.
Over-rated
Charizard - But wait, isn't that kind of hypocritical considering what I just said about Pikachu?
Not exactly. The main reason why I pardon Pikachu is because he's the mascot of the entire Pokémon series. Charizard is...one starter Pokémon in one generation (two if you count the Kanto remakes.) And he's not just over-rated by the fans, he's over-rated by Nintendo itself. Gen 6 not only gave you a free Kanto starter, but they gave Charizard TWO different mega forms. The only other Pokémon I can think of with that honor is Mewtwo, who is, you know, a legendary who's also a clone of what is canonically the ancestor of all Pokémon besides Arceus and the creation trio. And they not only made his X a dragon but also gave it the same color scheme as a Shiny Charizard. Yeah. We get it, Gamefreak! Charizard is a badass...flying, fire-breathing reptile that isn't a dragon! Alright already!
Muk - The only real reason why I think Muk is overrated is because people like it better than Garbodor. Garbodor, at the very least, is ugly and unpleasant in a unique and interesting way. It's a ruptured garbage bag...bear...thing. How many other games feature a ruptured garbage bag bear thing? Muk is a pile of nothing in particular. It's a blob, a thing that is defined by its lack of any defining features. It's a sentient purple booger whose life ambition is to eat Professor Oak. Not something I'd want as a pet, a friend or a bodyguard.
Salamence - Oh cool, it's a dragon with a mega form.
Rayquaza - Oh cool, it's a dragon with a mega form.
Garchomp - Oh cool, it's a dragon with a mega form...That's also a shark airplane. That's also...a ground type. For some reason.
Underrated
Conkeldurr - A bulky fighting Pokémon? Yes, please! If you can get over the weird veiny things, there's really nothing particularly "bad" about its design. I also really like the contrast between its super-serious expression and its big red clown nose. It's contrasting, yet it doesn't exactly feel out of place either. He just looks all like "...Yeah...I've gotta clown nose......DEALWIFFIT!"
Milotic - Yeah, surprise of all surprises, I put my favorite Pokémon on the list, and it's also not exactly a Pokémon that gets a lot of dislike. But allow me to change your perception of this Pokémon entirely. You know how the games often refer to it as the most beautiful Pokémon in the world? And you know how it's really pretty? And you know how it has that sort of serious expression that one might describe as sort of serene and majestic? And you know how it's actually a very capable defensive wall?
I would like to propose the idea that it's actually the Pokémon equivalent of that one really serious but really beautiful businesslady in every office who's exasperated over the fact that all of her colleagues are either ogling her or wishing they could trade bodies with her, when she just wants her project to be taken seriously and paid attention to. Once you see it that way, there's no unseeing it, and for some reason I find the idea of a giant moray eel with pink eyebrows being a grumpy businesslady both hilarious and oddly adorable at the same time.
Druddigon - Who cares that it looks like a chewed up flower...Oh? Everybody? ...well I think it looks cool...
Ho-Oh - In spite of how important this Pokémon is to the Pokémon universe, the only time I see anybody talk about it is when it's connected to random fan-theories, and the only time I see anybody actually use it is...never.