It's a system of checks and balances. The Presidential pardon power is specifically a check on the power of the Federal judiciary.

Regimes have toppled in response to popular uprising against imprisonments perceived as unjust. Having a system of governance without a way to rectify that seems unwise to me.

The check on Presidential authority, in turn, is impeachment. It's not a perfect system by any means, but in my estimation it's a good one.