Yes, there is no doubt
Let's Encrypt is a best free & automated SSL certificate provider at this time and gained great popularity, however free SSL has several drawbacks:
- Let's Encrypt offers Domain Validated SSL certificate only.
- Free SSL valid for 90 days with automatic renewal option.
- Let's Encrypt does not offer Organization Validation (OV), Extended Validation (EV), Wildcard SSL or multi-domain SSL certificates. (Note: They will offer wildcard SSL in 2018)
- You can not use free SSL for Email encryption and Code Signing for securing downloadable software.
- There is no warranty and Lack of customer's trust because due to no organization validation.
Whereas, Paid SSL certificates are issued by Certificate Authority (CA) such as Comodo, Symantec, GeoTrust etc. and these certificates are valid for 1-3 years. You can find different types of CA signed SSL certificates at cheapest price (price from approx. $5 per year) from authorized SSL certificate reseller/provider of CA. If you are looking for Paid Extended validation SSL certificates, then I recommend you
Cheap SSL Shop. So, you can choose SSL provider based on how many domains you want to secure with SSL and certain level of trust indicator that you want to display.