Telling the browser to accept all self-signed certificates is a bad idea, because it's no more difficult for an attacker to create one of those than the legitimate domain owner. Let's Encrypt has at least two huge immediate benefits:

1) It does challenge-response domain validation from an external server. It's not enough for an attacker to intercept and modify traffic between the client and server -- they also have to control the route between the server and LE. This isn't an infallible check but it dramatically raises the difficulty of an attack, especially if the check is done from multiple independent locations.

2) LE supports Certificate Transparency, which means they verifiably log all certificates that they issue to multiple third-party observatories. Even if an attacker can bypass domain validation, they can't actually get a certificate without immediately making it obvious that they've done so, giving the server operator the chance to revoke the certificate and investigate (if they're paying attention).