For a couple of reasons.

It's supposed to be an Executive check on the Judicial branch. And theoretically, the legislative branch can check the president with impeachment if he uses the pardon improperly.
But that doesn't work when all the pardons go out on the last day in office, or if he has a compliant Congress.
Again, theoretically a president could have a DC hit squad murder folks with the promise of no consequences.

And the way they are given out are unjust. The only way to get a pardon is if someone with influence advocates for you. Regular pardon requests get tossed out. But let a Kardashian say your name and you have a chance.

I agree with the way Obama did it for low level drug crimes. Just a blanket pardon for everyone meeting some criteria.