I really want to love Let’s Encrypt, but then I turn to StartSSL. In my case, I’ve a Class 2 validation, so I can issue wildcard certificates with two-year validity. While Let’s Encrypt is automated, the three-month duration is still an annoyance when different applications and programming languages use different CSR, key, and leaf formats. Add to that the need to enumerate every subdomain covered, and I’m prone to stick with StartSSL.
Also, StartSSL now has an API, which was one advantage of Let’s Encrypt. While I don’t issue certificates frequently enough to warrant such an integration, it’s a nice feature to consider for other StartSSL applications.
For me, it comes down to this: I use Let’s Encrypt for the fluctuating, random assortment of domains that I register on a whim and redirect elsewhere, while StartSSL is what I use for domains of permanence or significance. This isn’t a slight against Let’s Encrypt, it just doesn’t suit my particular needs.