Anko, Konan, and Mei in Naruto.
Anko is pretty much a really important person in Konoha, being one of the Chunin Exam head examiners, is very much trusted by the Hokages, and was once a subordinate of Orochimaru's, having been able to survive at least one of his experiments, and was (kinda) almost able to kill him. However, she was only around during the Chunin Exam arc (and even then her presence is sparse), and didn't show up again until a few hundred chapters later during the Fourth Shinobi World War, tracking down and doing battle with Kabuto (who's one of the two instigators of the war), she's promptly defeated and captured, using her to strengthen his own powers, and even being used to revive Orochimaru. She's then left in the cave and that's it. Her return role is very passive.
Konan was one of the founders of the Akatsuki, had a unique fighting style and power, and was probably the sole good person of the organization. She's shown to be very powerful, able to go toe-to-toe with Jiraiya... until he hits her with her pretty much only weakness, and she's out of the fight pretty quickly, leaving room for Pein to fight him instead. She then does about bugger all for the rest of the series (save for one bit, which I'll get to in a moment), even during the invasion of Konoha, she's just sits behind with Nagato and doesn't do anything. When she FINALLY gets to do something, she has a pretty epic battle with Tobi, but it's probably the shortest of the Akatsuki battles and she dies.
Mei is the Fifth Mizukage, is in possession of two rare and powerful abilities, and was able to take on Sasuke on her own for a time. However, of the five Kages, she's had the least development and page time, and outside of her battle with Sasuke, her abilities are almost never shown, not even when she's fighting with the other Kages against Madara!
This is what I hate about Kishimoto. He introduces these awesome female characters, and then goes nowhere and does nothing with them.