I don't think there are too many bad guys, it's just he's trying to develop all of the bad guys so that we can sympathize with them, but they end up dieing soon after their history is reveled! Wasted memory space.
There are four bad guys:
1) Madara.... Which is very very powerful.
2) Tobi .... Also very very powerful
3) Kabuto.... Another Very powerful opponent.
This three have been upgraded and hyped to the MAX..... They won't to destroy the village and dominate the ninja world.
4) Sasuke.... Now for sasuke he is a bad guy however I do believe he is going to change soon for a few reasons....... The chapter leaf ( when itachi talked about his sacrifices and what he believes in ) and that itachi is going to talk with sasuke and bring him to the good side.
I also don't think that Naruto and sasuke are going to fight.
The end result is...... There are too many bad guys in the story and they are all rooting for the same thing.
The worste Kisih can do now is kill of Kabuto easily, that would really destroy the story line of Naruto.
Oooohhhhh and there is one more bad guy who seems to be playing in the shadows alot.......... ORO. Yes I know he got sealed however Kabuto is turning into him more and more.
If kisih really wanted this story to be better he should have upgraded and hyped up a powerful good guy, or at least introduce a new character who is a good guy...... In my opinnion.