I just started reading the manga and watching the anime recently. So everything is still a bit fresh for me.
Kakashi is addicted to pornography. We've seen him at it late at night, until daylight. With it are activities that I leave to the reader's imagination.
It has affected his stamina, that is why he couldn't store much chakra. :shrug:
The saying "an idle mind is the devil's playground" is true.
Before Team 7, he was an ANBU operative so that kept him in his toes enough to develop as a world famous/infamous shinobi.
At Team 7, with a lot of idle time and baby level missions, he discovered pornography and got addicted. His skills plateaued.
God came and saved Kakashi in the form of Pain. The death of Jiraiya was a jolt to everyone. Kakashi got worried and started to abstain, in order to train.
Pain destroyed the village and in the process included all his pornographic materials. Without all that pornography and no private area "to do some stamina draining activities" plus the disaster brought him back to a state of razor sharp professionalism. So from a plateaued state he is back in rising form.
As for his excuses to his students that his chakra is limited because of his sharingan is not true. Just look at how he made excuses why he is always late. Open your eyes, any sensei who is addicted to porn will always blame his sharingan for always being tardy, having little stamina, energy, and chakra. It is God's 11th commandment, "thou shalt not admit usage of porn." I wouldn't blame Kakashi either...