For everyone that complains about Let's Encrypt, I just want to state that Let's Encrypt solves the single largest use case for issuing certificates for domains - a single server you control which hosts one (or more) website(s). All of these issues with 3 month certs, rate limiting, and limited certs/domain stem from much more complicated problems and it isn't fair to expect Let's Encrypt to tackle those.
Wait, what? How does the 3 month cert limit stem from a much more complicated problem? The 3 month cert limit is an arbitrary limit by Let's Encrypt, and has nothing to do with a more complicated problem. They could just as easily make it 6 months or a year, but instead they chose 3 months.
Broadly speaking Certificate Revocation is garbage. It doesn't work. So when a bad actor generates a bad certificate there's a legitimate chance that without Certificate Pinning, that Certificate will be accepted even if theoretically revoked. A three months max duration limits the potential liabilities to three months.
Additionally three months offers the better theoretical security against state actors. While a 2048 bit key is normally considered to take tens of years to break, it is possible a state actor with unlimited resources could construct a quantum computer that could cut that time down significantly. If the certificate pair is regenerated every three months using a safe cryptographic source this makes breaking it likely not worth while even for a quantum computer.