Not to be rude, but please could you discuss the Eclipse stuff in your own thread? I'm trying to get some feedback on my IDE here.
As for combination: you can have multiple ino/pde/cpp/c files and include libraries easily. I'm using MultiWii myself for my Quads.
One possibility that I think would be fitting is to use the Arduino preprocessing on ino/pde files and not to do it on cpp files.
In my opinion, having the preprocessor is not a bad thing pre se, but it's also not helpful if you can't see what it's doing.
So why not make a automatic header file, that's updated whenever you save a file in the project, which contains all the definitions.
This way users can see what's going on and learn from it.