The most underrated pokemon is magikarp, I mean it is the most powerful pokemon, the Water temple even uses it against Link and nearly wins. Link would have won easier if Navi (Tatl) had known self destruct though.... on a serious note, there are some pokemon which get a bad notes about them and actually deserve it, like bidoof, they already had rattata which looked kinda cool and everything then suddenly they bring out a lame-*** looking beaver-thing and expect people to like it? what were they thinking!
As for an underrated pokemon, hmmmmmmmmmmm, nothing I can really think of besides magikarp though, and therefore feebas, both pathetic pokemon but turn into quite powerful creatures at that. Possibly also Shuckle, nobody probably uses it but it apprently has one of the highest defences.
There are a lot of Pokemon that are underrated that's for sure, but I think a surprising one is actually the Purlion and Liepard lineup.
While yes, many people tend to like the Pokemon due to the design, It's surprising to hear how much they are disliked due to poor stats. I have a Liepard named Leona, and while yes, she has been one of the more difficult Pokemon I have trained in Black Version, she is still an important asset to my team. I've finally figured out a move set and strategy for her so she doesn't always get knocked out by special attacks so quickly.
I don't know, I think any Pokemon can be pretty boss when given the chance. It is a shame that people can't get passed appearances or stats sometimes (and I speak for myself as well.)
In the Competitive scene I'd say that Flygon and Leafeon are very underrated. Of course we're not all competitive buffs here so I'm gonna go ahead and say that Pokemon like Pidgeot are. According to it's Pokedex entry it can fly at Mach II !!! That's very very fast.
I think most underrated pokemon are 2nd evolutions from the starters like charmeleon,wartortle,croconaw,Bayleef (best),and marshtomp i think bayleef is underrated but i like him cause his looks not cause stats and moves!
i've only played Blue/LeafGreen so i'm going to go with Hypno. when people go for psychic they tend to choose Alazakam but Hypno has much better special defence and decent special attack, plus he can learn Hypnosis, which Abra/Kadabra/Alakazam doesn't, which makes Dream Eater MUCH more useful
Golem. Not many people use him as far as I know because of his many weaknesses. The Same with Gyarados and Magikarp. Nose pass/Protopass just ignored a lot. Depending on the person, most of the newer generations, period, have less users than the older ones.