RE: "Who only issue 90 day certs and who's tools don't work the on 50% of websites that run IIS."
What's the problem with a 90 day validity time? Let's Encrypt renewals are automated, you could renew daily if you wanted. The extremely long 90 day period is partly to reduce server load and partly to allow for intermittent failures in the renewal process.
When you say that the tools don't work on 50% of IIS websites... It would appear that there are automated interactive tools for IIS, as well as the same choice of command line options as a linux system. What is the problem?