Limiting a bit the impacts if Let's Encrypt is compromised in any way.
If Let's encrypt is compromised, either by being able to issue certificate for arbitrary domains or if the CA itself is compromised, the impact would be huge given the current number of certificates signed by it and this number is likely to grow in the futur.
With several CAs in different organizations, you have a far lower risk of seeing all the CAs being compromised at the same time, thus limiting the impact of a CA being compromised.
Note that it doesn't mean a full decentralization, but rather a set of CAs (5 or 10) independent of each other and providing a service as conviniant as Let's Encrypt.
As a side note, an idea a colleague of mine suggested to extend and better the security model of CAs/certificate would be the ability to have a certificate signed by several CAs.
Let's say you are a bank or a security sensitive website, you could have your certificate signed by 4 or 5 CAs, and then, you could publish a policy, for example in a TXT DNS record, stating that you need at least 2 or 3 valid CA signatures. This way 1) your certificate doesn't need to be renewed in emergency if its CA is compromised, 2) if a CA is compromised (without people noticing), it reduces the overall impact as an attacker would have to in fact compromised several CAs to actually exploit this (MiM or impersonating websites).