I would like to see official support from Cloudflare through the release of a server administrator configurable Auto SSL provider. As of now there are two available for server admins; cPanel w/Comodo, or LetsEncrypt. I think it would be awesome to have Cloudflare offer this as an official “AutoSSL” provider, even for domains not using Cloudflare for HTTP proxying.
I doubt this will happen. It’s far easier for Cloudflare to support it if its running off their servers and SSL is available in the free plan so there’s very little reason to not have users sign up their website for a full proxied account. If for whatever reason you don’t want the full Cloudflare experience, I’d say just go with LetsEncrypt. They’re also free.
Full disclosure: I am speculating, I’m not involved with Cloudflare’s decisions.