Pehaps Naruto is stronger and has more chakra than Kakashi but that`s not the only thing that influences the outcome of a battle. Kakashi is way smarter than Naruto.
And Kakashi is not dead. I don`t know why everybody keeps saying that
After being saved by Ebisu, someone else has to step up and save Konohamaru. Konohamaru could try something but just enough so we see that he is not afraid and that the will of fire lives on in the next generation as well. Now, I wanna see Neji saving Konohamaru. Damn it Kishi, where is Neji

I believe that Kishi has to bring in Neji, Shino, Lee and other into the fight. We haven`t seen Shino in a long time, since the Madara encounter.
Naruto has to learn to cooperate with Kyuubi! I see no other way
1.) Naruto can perform jutsu and learn jutsu that Kakashi can't. Does that necessarily translate into a victory, not necessarily. Naruto is
becoming stronger than Kakashi, and will be much stronger. Naruto is not dumb, and I think that learning patience and balance will allow him to think through situations with his mind rather than just his emotions. Naruto does have a massive amount of chakra and durability (much stronger with sage mode), and Kakashi's chakra level is his main weakness, especially with his Sharingan.
Naruto's possible improvements:
- patience/balance with emotions for a clearer mind
- Sage techniques (i.e. jutsu), toad-fu (taijutsu) and speed, and whatever that massive jutsu is, improved summoning accuracy, reliability, and diversity (don't make me beg for the toad stomach).
-Fusion, which I think will happen (Kishi is just using this to buy time)
-greater durability (I expect wind element rasengan is usable now). Remember Naruto fell that massive distance during training and was not hurt.
2.) Kakashi is near death and will be saved by a slug is my guess.
3.) The way the Kyuubi will cooperate with Naruto is if he respects him. Currently he believes that Naruto is pathetic and can't do anything without him. The Kyuubi initially cooperated because Naruto demanded rent. He didn't ask and wasn't afraid. Respect is the key to the Kyuubi's cooperation.
4.) I expect to see the Konoha 11 (chounin, Neji) show up soon. Fukasaku said that the key to defeating Pein was to fight him one-on-one. Given that Pein has interogated a large number of shinobi and found out noone knows or will tell (which is a hell of a lot more than the cloud shinobi), he should focus on protecting his secret and leave.
*Foot note:
*Kakashi didn't use MS against Kakuzu, since Naruto and Yamato arrived in time.
*Given that each generation surpasses the last, Naruto will be surpassed as well.
* If I repeated someone's above statements, I credit you.