Rock Lee is definitely not underrated. He's a dropout similar to Naruto as a kid but he's developing superbly into the next taijutsu specialist of Konoha. If you want to get technical Rock Lee isn't even a "prodigy". It's debatable that he is a "prodigy of hard work" (I believe this) as Guy states, but personally I don't think Lee belongs in the thread because I don't think he's underrated at all
My 3 in no particular order are:
-Haku. Had no help discovering his Kekkei Genkai and developed Ice techniques on his own. Truly tragic that he couldn't have developed further. He would have been a remarkable shinobi.
-Neji. He's a branch member of the Hyuuga clan, yet, he developed and mastered the Hakke Rokujuuyon Shou and the Hakke Kaiten
by himself. Traditionally they are taught only to the main branch but Neji discovered these abilites alone. Even as a branch member he possess a skill great enough to rival the main branch family. Since his fight with Kidomaru he hasn't received any spotlight
-Sasori. As people already said, he was a genius puppet master who created dozens of original puppets which are still used by puppeteer today. He killed the strongest Kazekage in history and developed a technique of greater magnitude than even Chiyo's 10 Puppets. If he had fought anyone else other than Chiyo then he would still be alive today. The only reason he lost was because he let Chiyo kill him.