Let's see here Hiro went into the future twice in the first season and made changes by returing to the past, he made one trip to save the waitress and failed. But if he went back and removed part of the formula from the safe before he opened in the past then Arthur wouldn't have his half of it. Even future Peter altered the past just by going back in the first place. Plus we've had both Peter and Hiro going to the future and seeing a city destroyed or emptied, the only way around that is take away their power, if only for a short time.
As it stands, right now, Peter's powers have been removed. Completely. They're gone.
They can't make up their minds whether or not Sylar still has the powers he gained before Hiro nearly killed him other than telekinesis and intuitive aptitude.
Hiro is conciously deciding not to use his powers to the fullest. Which is, I might add, a better way of dealing with the problems you mention than taking those powers away.
That's three major characters who have been, for want of a better term, nerfed. Ruined. May as well kill them off.
I don't want to watch a show about a goody twoshoes hospice nurse, the CEO of a Japanese company who doesn't know how to run a business and an insane watch maker. Those people aren't interesting. Give them superpowers and see how they use them. That's interesting.
I don't know how often I have to say this - they already gave us reasons why Peter can't just replace all the other characters and why Hiro can't just float about in time whenever he likes. They did that in season one. Future Hiro specifically said "I am risking a rift just by coming here" when he delivered the message to Peter. Potential damage to the space-time continuum is a very good limitation.