If we are talking about back in the day, before we knew anything we do now...
Sakura was one of the things I had wished they didn't toss aside.
Ino was another character I wish they expanded upon
I would have liked to see the academy days a little bit more
I wanted to see Uzumaki and Hyuga clans more
I wanted to see more of the Narutoverse before the founding of villages (showcasing the war starting/blood thirsty side of the clans)
I would have liked to see more of Orochimaru and his past (maybe his parents or at least one of them)
With the knowledge we have now?
I still say Sakura should have gotten less nerfed in part 1 and most of 2
I wished they had touched more on Otsutsuki earlier
Would have tied in the whole incarnate thing sooner
Would have given Hanabi and Hinata less nerf and more development/feats
Would have focused a little more on relationships so the ending didn't seem odd
Would have liked to see more unified squad attacks and combo attacks from a person combining their own abilities like in Boruto