Well if Madara doesn't exist it doesn't necessarily mean the Uchiha Clan Massacre doesn't occur, because there would still be tensions between the Senju and the Uchiha (BZ manipulated things but this doesn't mean these two clans wouldn't be in a rivalry regardless, they're two highly powerful clans that probably clashed over things like territory or whatever)
Danzo still exists, Hanzo still exists, arguably even if Minato would have been better about keeping the Uchiha/Konoha tensions from getting too hostile, Danzo is still well-networked and subversive within and outside of Konoha
Hanzo doesn't die, because Nagato doesn't ever get Rinnegan (since Madara never attained them to give to someone)
Itachi is possibly still forced to kill his clan, Sasuke is still seeking revenge, gets up to EMS level
Orochimaru still exists, Shukaku is a bigger problem if Naruto doesn't have the Kyuubi
Final bosses are probably Hanzo and Danzo, which would be interesting
The manga becomes a darker manga with Sasuke as the anti-hero protagonist, and Naruto is a side-character
