The structure of the whole C3 runtime is fundamentally different and I think there are too many differences to try to list in full. For example just the fact not everything is in one file any more means you have to refactor code that uses a shared scope. The approach we took to porting our own addons was to take the SDK template and rewrite the addon from there. The new structure is a lot better organised so often you can make structural improvements as you go too.
The new C3 runtime is designed to be 100% compatible with the C2 runtime, so all the same capabilities are there, it just might be renamed or moved somewhere else. For example where you might have previously done glw.quadTex() to draw something, now it's renderer.Quad3() - it does the same thing but the names and parameters are different. Also, it's exactly the same API as the editor uses, so now you can have drawing code that works the same in both the editor and runtime!