Let's Encrypt cannot issue EV (green bar) certs, wildcard certs and certs with a validity longer than 90 days. While these are good features for many applications (i.e. a typical hosted website), there a lot of cases where that's not optimal:

- EV (green bar) certs are required to increase customer trust (it may be mostly snakeoil, but the CA system is heavily flawed and we are still forced to rely on it anyway)

- Applications where certs are used on other platforms than web servers (e.g. embedded devices, routers etc.) and 90-day renewals are not easy to implement in an automated way.

- Wildcard certs are mostly useful for convenience reasons, e.g. to easily secure a changing number of hosts within certain (sub)domains/zones (especially when they are only or mostly used in internal networks). I agree that the need for wildcard certs is greatly reduced with let's encrypt and acme.

I have a site that creates a subdomain for each new enterprise account and all subdomains relay on one StartCom wildcard cert. Ultimately, I can write a script to create a let's encrypt cert for each new subdomain but I've got plenty of other work on my plate at the moment.

Multi-tenant systems, for example, where each tenant gets their own subdomain. Let's Encrypt still has rate limits in place.

Not the parent, but wildcard certs are necessary for compatibility with clients that don't support SNI (ex: IE on WinXP)