One reason that can explain this is the need for 'power' or 'skills' decreased over time. Whenever there was raging destruction and war, powerful shinobi emerged to sustain the survival of their respective clans. After Hashirama and Madara established the leaf village, peace and prosperity spread everywhere, as more peaceful villages emerged. This was explained in one of the recent manga chapters : people took the truce between the most powerful clans as an example and decided to take a break from war. With no raging battles or major wars, the need for highly skilled shinobi declined and people started exploring other professions.
My guess is that Rikudo Senin was born with certain special skills and trained unimaginably hard in his generation to overcome the terror of the ten tails.
This also explains why Naruto and Sasuke have trained so extensively on the way to become the most powerful of their generation. The experiments of Orichimaru in reviving the dead, the Akatsuki's goals and conflicting views of Naruto and Sasuke were indicators of a potential major war coming up!