I always was of the mind that the file storage provider should have been the plugin, and that database-backed storage should have been the first-class citizen. The manageability of it, especially for hosted solutions (think: file permissions) is significantly easier and safer.
ASP.NET roles/etc should also remain a plugin, honestly, as it's another thing that requires server-side setup and may not be available to all users.
Basically, if this application can be self-contained (aside from its storage solution), that'd be ideal.
And, to address the storage solution potentially not being available for some (who the heck has a host without database access?), SQL Compact is an excellent answer.
But, since we're starting from v3, file-backed storage is a first-class citizen, so let's at least fix whatever issues with it you have. Maybe post an issue on github for it so we can track it? We can assess how to handle what as first-class storage citizens later on, once we take care of more pressing things like current outstanding bugs.
I'm also definitely a fan of simplifying or completely changing the internationalization system in the project. For people who want to run precompiled builds, it's not very practical. I really feel like the internationalization features should be handled via a plugin or language pack concept, like most other software out there.
I'm setting up a jenkins server right now with vs/msbuild/nant support and tied to the github repo, so there will be CI for this project.