Wow, an objective thread from you for once. That's a change.
I have very few criticisms for part one.
1) It would have been nice to have Shino and the Kunoichis in the rescue Sasuke arc as well as possibly a few more sound ninjas.
2) Since Sasuke had already learned an element, I think it would have been nice if Jiraiya had also taught an element to Naruto.
3) I would have liked Baki and Genma to fight each other and for them to be pivotal to the plot in both the first and second half.
4) I would have given Sakura a clan and special technique.
I have a few more for part 2
1) The biggest criticism I have is most of the K11 being cut from the plot throughout shippuuden. I believe that if Orochimaru had survived longer, or at least his faction led by Kabuto, that could have fixed it, as well as each of he Akatsuki having either subordinates or three man squads. Most of this could have been done in the Sasori/Deidara, Sai, Hidan/Kakuzu arcs as well as the Pein arc.
2) I would have kept the Pein avatars alive except for maybe Yahiko and developed them into characters.
3) I would have developed Hidan's backstory, techniques and extended his fights, which Kishimoto was forced to cut by his publishers and editors.
4) I would have given Naruto a legendary weapon to parallel Sasuke's Kusanagi.
5) I would have eventually shown Sasuke's training with Orochimaru, development of his Chidori and Sharingan and obtaining his Kusanagi rather than leaving it off panel/screen.
6) I would have had Konan fight most or all the chuunin kunoichis and possibly had her kill one or two. This scenario was actually shown in an anime opening.
7) Obito has grown on me and I believe he was well-foreshadowed, although I believe he being either Naruto or Sasuke from the future , Shisui or Fugaku would have been a great twist as well.
8) I would have had Killer Bee teach Naruto swordsmanship.
9) I would have given the seven swordsmen of the mist their own arc in the war and made them pivotal to the plot. Giving them Akatsuki level abilities and fights, having Sasuke and Taka fighting them and Mangetsu combining all the swords into one and revealing it was Hagoromo's, which Obito would have then preceded to steal.
10) I would have made edo hanzo and sasori far more formidable as well and given Mu, Chiyo and Kimimaro closure fights.
11) I would have had Naruto and Sasuke invent their own jutsus from scratch like Kakashi and Minato.