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.