It's all speculation at this point but my guess is that only the official plug-ins will import with the project from C2 to C3. Currently you can't even upload to the Scirra arcade if your project uses non-official plugins. Hopefully I am wrong though as many of our projects rely on community plugins.
Are you sure about that?
Some of my games on the Arcade use third party plugins, and they work just fine.
I believe C3 will have an extended javascript API with backward compatibility, so any plugin written for C2 will work for C3. There is no difference between official and third-party plugins. At the end of the day, they are both javascript code that calls the same API.
The C3 engine can be more powerful and feature rich than C2's, however, from a software design perspective, it is very possible to keep the same API, or at least, to keep the same function names and variables for backward compatibility. I think Scirra will not be as stupid as to change the API in a way that it breaks the hundreds of plugins made by the community.
Personally, It doesn't really matter to me. I regularly maintain my plugins and I'm ready to migrate them to C3 as soon as I get my hands on the SDK. If the API stays the same, that's good. If they improve it despite breaking compat, that's good too, the old API is limited in many ways, we have limited editor control, limited or at least undocumented access to other plugins in other objects in the layout, it is impossible to create an object from scratch, we can't manipulate layers, or trigger the loading of another layout. Plus, Javascript is a terrible language, programming in it should be outlawed as it is almost a form of torture, but we're stuck with it. There is a reason why almost all serious game developers who use Unity prefer C#. I digress, sorry.