Bad Chakra Control.
Bad Ninjutsu skills.
NO Genjutsu or counters.
Fuinjutsu should be the last thing on his mind.
1) Are we reading the same manga? This was thanks to Kyuubi messing up. Naruto since he got RM is possibly the ninja with best chakra control in the entire series and he just keep getting stronger in that respect, he is 1 step from having a partnership with Kyuubi like Bee does.
2) I will recognize that the versatility of his arsenal and variety is very lacking he only have rasengan variants and clones. But BAD ninjutsu skills?! Are you kidding me?! He can spam rasenshurikens now, destroyed a forest and is on the verge of being able to cast and eventually spam the Narutoverse's version of a nuke. Plus he can use Kage+ level clones, remember he is on the verge of having a partnership with Kyuubi so he will be able when fully rested to create an army on the HUNDREDS of Kage+ level clones.
3) With this I agree, however again he is on the verge of making a parnetship with Kyuubi, his genjutsu defense problem will be solved by that.
Your points are not overall wrong (except point 1), however the thing is that most of his lacks are going to be removed when he gets a partnership like Bee and Hachibi. His chakra control is already excellent, and when he gets the partnership he will be able to cast Kage+ clones on the hundreds at least and spam Bijuu Damas.