Before making this thread, you should atleast have thought the reason for decreased clones! In Sage mode, he has to maaintain it as .while he is in movement, it will disappear at a moment! While in Kyuubi-SO6P Mode, he will not have this problem as the Kyuubi gives him a continous enormous chakra reserves! He could have made 10000 clones in Sage Mode but he knew that Sage Mode effiiciency is its durability!
If Naruto completely masters his Kyuubi-SO6P seal, I think he could perfection his Sage Mode and create 1000 clones to fight and 1000 to absorb Nature Energy (along with the Flying Thunder Technique, Kyuubi pwer and ninjutsu)!
Still, Naruto will become very powerful but I don't find him with a complete advantage compared to Madara (MS and Rinnegan power)! It goes the same for Sasuke! Despite how many new powers Naruto and Sasuke, Madara is still more powerful according to me! Yeah, if Sasuke and Naruto could reunite their forces, then it could be a different story!