Before I start with this post, I just want to say that I love what Let's Encrypt has done to the SSL Certificate market and think that its well overdue.
However, as with everything in life there is a use case for everything and even though Let's Encrypt is a wonderful service there are still use cases for the other SSL Certificates that are on the market. Again I'm not trying to sell you an SSL Certificate I just wanted to clear up my thoughts on the use of SSL Certificates.
Let's Encrypt offers free Domain Vetted(DV) SSL Certificates and recently Wild Card Certificates, now if you are running a Blog Site or a non commercial web site this would be a great fit for you as running your web site in HTTPS mode has been shown to help increase your rankings within search engine results.
That said if you are running a commercial site where people are looking at buying items from you. You will need to look at the level of insurance that you will get and the level of trust that is shown to your customer.
A Domain Vetted SSL Certificate will only show the padlock icon in the address bar as shown here:
Extended-Validation-SSL
Also Let's Encrypt offers no insurance on their SSL Certificates, where as depending on who you use to buy a certificate from you will find that they all offer an insurance or a warranty of some form.
Once again I would like to say that I have nothing against Let's Encrypt and if you were to ask us about our offerings on SSL Certificates we will always start off by seeing if we think they are a fit for you hosting needs.