but still, Pein is following the Madara's command. So would say that Sharingan is much more power ?

okay then, not say that is Madara, say its man-under-mask-with-sharingan. 

I think Sharingan more powerful, cos Tobi is still the mastermind of Akatsuki.

i read a short text on sharingan in narutofan.com. It seems that prolonged use of mangekyou sharingan will damage its user's eyesight eventually. Does it mean that itachi is no longer as powerful as he once was? Does it mean that it damages tobi's eye so badly until he has only one eye available now?

Maybe the fact that byakugan is better than sharingan in the sense that byakugan does not harm its user. However, so far, there is no other higher tier skills unlocked for byakugan user yet.