1. Itachi
2. Shisui
3. Minato/Kakashi/Jiraiya
After reading some of the comments in different discussions it seems like I'll get skewered for choosing these three.
I feel like all three were extremely important to the show in their own way.
Itachi saved the village more than once (Killing his parents/clan, releasing edo tensei, sort of double agent for konoha/akatsuki) and sacrificed so much all for the sake of the village. Amazing skill wise (suanoo'oo with totsuka blade and yata mirror while nearly blind and dying from an unknown disease). His love for sasuke and the extent of what he did for him is amazing. Made him hate so that he could become more powerful and periodically checked in on him to make sure he wasnt in any real danger. And then did alllll this knowing he'd be branded the biggest hidden leaf traitor. Overall his selflessness is what really gets me.
People love to screw with Shisui cause of his lack of screentime but he's pretty important. Without him I feel like Itachi wouldn't have fully become who he did. He's the one who taught him how real ninjas fight from the shadows, and shared overcoming the curse of hatred. It sucks that Kishi limited him to an episode and Danzo taking his eye so quickly. The Koto-Amatsukami really could have worked on the clan and saved the slaugjtering, but naa, Danzo being the prick that he is had to ruin that before he even tried. Power wise, I think his MS is the dopest power plus the combination of the teleporting. Danzo was playing Mifune like a puppet before Ao said something about it and he had just ONE eye. Turns out Kishi gave Shisui a Susanoo'oo for the next game too which I think is awesome and an attestation to his power that we perhaps didnt see, but some people gripe about. He sacrifices himself in front of his best friend after giving him his other eye and leaves so little a trace that he was actually safe from Edo-Tensei the whole time unlike... Every dead person in the series basically.
Last but not least, Minato. This is the one who most people have a problem with but I feel like its more of a circumstance of Kishi not showing enpugh from him. Hes a true genius that died way before his time and then even after bringing him back, Kishi went ahead and ripped his arms off...he pretty much perfected the seconds flying raijin and thought to create rasempnan after seeing tailed beast bombs. Hes good on Sage mode and can even control Kurama's chakra after coming back to life which again I feel like is an attestation to his greatness. Its unfair to compare him and Naruto, seeing as to how he's basically become a god with all the powerups.
Jiraiya and Kakashi I feel need no explanations lol.