There are a couple of reasons for the short lifetime. Our goal is to increase HTTPS usage on the Internet. Part of that goal is decreasing the incidence of avoidable certificate errors, like expiration. Since expiration errors are very commonly caused by human failure, we want to encourage people to automate renewal of their certificates. A ninety day certificate lifetime is a part of that encouragement.
However, for people who still would like to manage certificates manually, I think there is a good argument that a person gets better at a task they have to do six times a year than one they have to do once a year. People are less likely to make mistakes, and more likely to set up reminders and make sure there is backup for when they are on vacation.
@questiontradition: The stock Let’s Encrypt client is configured to attempt renewal at the sixty day mark, with thirty days left before expiry. If it fails, it will send email and the system operator will have a month in which to intervene and correct any problems.