I know they could potentially do cute de-duping tricks on their end, similar to tarsnap, but even if they passed those space savings on to me I'd still lose the file-level features.

That's why I chose EncFS to begin with, and asked for potential other file-level tools to replace it. Realistically, I'd prefer if this expedited EncFS 2.0 and 2.0 fixed the noted issues.