Overrated = didn't enjoy it as much as others did
Underrated = Felt it was better than what others thought
Because you really can't argue against the popularity of a series, and it all comes down to your own personal likes and dislikes. So it obviously can't be put into either category based on views of the majority, but rather just by oneself or a few. So no one should take any of this seriously.
On that note, here are some of my personal list of shows that I didn't like as much as others:
Akira is one of the few I thought was overrated. Even when I first saw it in the 90's, I was like ok this is cool, but why is everyone going nuts about it, bigger question is, why do people still go nuts over it?
Naruto (the anime) is also overrated. The hype was deserved when the show first came out, and for the first 60-70 or so eps. But now it's blah and fillers.
Totally agree.
Akira - Kept me away from anime for quite a long time, when an otaku friend tried to convert me with this boring movie.
Naruto - I really enjoyed it when it started, but the later fillers and Shippuuden actually made me angry. Some of the worst storylines and animation of the latest years (I swear that it keeps getting progressively worse). It's hard for me to believe that people still follow it..well, actually support such blatant milking of fans (sadists).
I'll add Cowboy Bebop. What story? It's an episodic series with nothing worthwhile to remember. My guess is that it having a westernized feel allowing many newcomers to ease into anime, and it being a fav just by being one of the first.
What I feel are underrated or not seen as much as others:
Hikaru no Go - Many avoid it for being a long series and/or being about a board game. But it has some of the best character development and supporting cast with anime. Even though there is a ghost involved, it's one of the more realistic. Forget about it being about a game/sports and just watch it.
Princess Tutu - I'll admit that it's not for everyone, but hearing others claim how great the classical music is in Nodame should also check out this series. This bittersweet fairytale is not meant only for kids. I enjoyed the comic relief and loved the art style.
Kino no Tabi - I bought the slimpack set as soon as it came out. The episodes make you think long after it's over and Kino is no cookie cutter anime character. Quite fitting for someone to not prejudge different social standards.
Tytania and LoGH - Can't get any better than this for space operas in anime. Subtract Code Geass' over exaggerations and plotholes for more realism. But I can see those who don't like reading long dialogue to not fully enjoy it. Plenty of action only type elsewhere.
Toradora! - It is boggling that gg would drop this, but not everyone there felt the same since qq continued with it. I don't feel it yet should be called underrated. Like Haruhi, it will gain greater popularity toward the end and/or after the series is done. Toradora! is not just another tsundere show, it has a great script and a very likable cast.
Some other recent anime that I'd expect to be more popular: Casshern SINS, Hyakko, Eve no Jikan, Kara no Kyoukai, and Skip Beat!. But should wait and see, as more word about them goes around.