To add to Jasper's fine answer...
Fourth major benefit of pardons:
Presidential pardons are about checks and balances. The legislative system has determined a law, the judicial system has determined an infraction of that law, and with a pardon the presidential system can react to a mistake made by either the legislative or judicial branch.
Additional constraints on pardons:
There are no formal constraints on the president to pardon federal crimes, but there are many informal reasons why a president will not pardon a convicted person. These may be personal beliefs and moral constraints as well as the repercussions viewed by giving a pardon. For instance, people may come to dislike the President's pardon and penalize the administration or his/her party by not voting for them in future elections or helping finance the opposition. There are many reasons why people may come to dislike a pardon, including conflicting beliefs about the type of crime committed or framing by other political parties.