Here are my biggest moments:
After the zabuza arc: It was the only mission they did not central to the overall plot. And I liked that. I wish they did more just normal missions in the series. Back when they were ninjas for hire, instead of these peace soldier guys.
After the Chunin Exam arc. It was still just another trial in the lives of ninjas. Wish they just continued with normal missions after.
After sasuke left. That arc was so damn enjoyable. It was a REAL MISSION. Shikamaru was great. Everyone's fight rocked. Wish after sasky left, they returned to those things.
Regrettably, shippuden was ENTIRELY revolved around the central plot (akatsuki, moons eye, sage of six paths, sasky being evil and shib, itachi doing his itachi thing etc). But that being said, it still had cool moments. If it ended after pain, it would have been great
They could have done a short epilogue after: sasuke killed itachi, became good again, itachi stayed a bad guy. Naruto is the village hero. Tobi never became the main villain. Jiraiyas death was perfect to have at the end. Because then naruto masters his sensei's technique to defeat the akatsuki leader. And he won WITHOUT kyuubi (for the most part, you know what i mean. He was strong WITHOUT it). Good ending