90 day limit is to encourage automation
If you only had to renew certs every year, a fair chunk of admins wouldn't even bother installing a cron job to run the certbot script to do auto-renewals. One of the major goals of Let's Encrypt is automation - get the initial cert and then forget about renewals because a cron job will handle those automatically (if the renewals fail, Let's Encrypt will email you automatically if expiry is getting close for any cert). A short expiry period really does focus the mind on getting the automation working.
I think Let's Encrypt is an idea that's been long overdue - the commercial secure cert market is a licence to print money, especially where the entire process is automated and rarely involves a human on the cert vendor side. As for Extended Validation certs, this seems to be an excuse to charge double for one or two extra checks that probably take less than a minute each...