underrated:
lucario (ONLY COMPETITIVELY) - luke's actually a fun pokemon to use. swords dance, close combat, extremespeed and bullet punch means it's a nice late-game cleaner. +2 close combat hits very hard, and extremespeed + bullet punch are usually strong enough to clean up offense. lucario's steel/fighting-typing also means it can survive a hit or two, despite its poor bulk.
rhyperior - this was obviously coming. people shit on it due to its design and typing, forgetting that dragonite for example also looks really different from its line. on the competitive part, rhyperior is by no means amazing, but can function as a hard-hitting tank which checks birds and charizard x, and the SD set is a monster in trick room.
politoed - rain is still cool despite the fact that drizzle is no longer permanent. it usually supports its team with damp rock drizzle and a defensive set, or it can go to town by throwing choice specs hydro pumps. on the non-competitive field, many people forget this thing even exists lol
salamence - a surprisingly versatile pokemon that can go mixed, DD, scarf or defensive, which is supported by its good attacking stats and movepool, as well as intimidate to allow it to set up easier, or moxie for the scarf set. its downside is that it's pretty hard to use and steels, fairies and weavile can be jerks to it (although it has ways to get past them, bar weav). as for the mega, people don't like it due to its design. yeah it's kinda ugly lol, but i care more about its battle prowess, and anyone who has played ubers knows this thing is just ridiculous
overrated:
pikachu - obvious reasons.
charizard - obvious reasons. zard X and Y are great on the competitive side, but aren't mega-rayquaza level.
lucario - severely overrated unless we're talking about the competitive side. i swear every lucario which appears in fanfics has aura and is ridiculously powerful. it also took the spot in brawl, which mewtwo should have kept.
eevee and its evolutions -
http://www.pokecommunity.com/showthread.php?t=355771
manaphy and hoopa-U (competitively) - never understood what makes them so great. they obviously have the power to break through balanced and stall in theory, but usually stall can adapt with unaware quagsire, gothitelle, chansey (manaphy and NP hoopa-U) or skarm (physical hoopa-U) while balanced has room for a pokemon who can revenge kill them. the fact that offense is the most commonly used playstyle is not fun either.