Fullmetal Alchemist:
I really expected a lot from this anime because the manga is so brilliant, but they really dropped the ball with this one. I understand they couldn't do a full adaption of the manga due to a lack of chapters, but the direction they took the series was absolutely inexcusable. After about 20 episodes it starts to separate from the manga, and it shows, the story suddenly just becomes slow and boring, the characterization is dulled, and they couldn't even do a decent villain to pull everything together.
Dante was the worst anime villain I had ever seen, she did nothing but talk. This is ok if you've got good writing and the villain is actually saying something meaningful, but all she did was smacktalk. In the end all it took to defeat her was for Al to decide not to let her kill him (He didn't even have any reason to let her do it in the first place.)
It's also really sad that so many people refuse to watch Brotherhood when it's imo one of the most perfect animes ever created. They seem to think the first one was better due to it's more serious themes and gritty mood (baffling since Brotherhood was way more mature in theme). Most seem to give up on the new show after a few episodes, because those 8-9/10 episodes weren't as good as the 6-7/10 episodes they remember through rose-tinted goggles.
Naruto Shippuden:
Not really much to say on this, they just messed it up big time, it's really rare for them to get any scene right in this production, while for the original Naruto it was generally spot on. Naruto was quite fast paced and exciting, while in Shippuden it just seems slow. Really weird when you consider the manga counterpart of Shippuden has a lot more action going on. That coupled with the fact that Shippuden burns through chapters faster than Naruto, I just blame the directorial staff, it's a bad adaption. I haven't watched every episode due to it's lack of quality, but I've still seen a lot, episode 133 remains the only perfect episode.