Several root programs have stated they're not interested in expanding the supported algorithm set, so there's no path towards pushing this, and nothing Let's Encrypt can do.
Ed25519 does have one big disadvantage, which is that it's not a prime-order curve, so there's risks around low-order points. The NIST curves have good complete addition formulas now, and there's high quality implementations that exist. Thus there's not any significant advantage to switching curves, and compatibility problems would stay for many years.
The big interest for new algorithms is in post-quantum algorithms, which represents a significant new research and development area.