C2 should handle large games just fine in future - your projects save to folders for collaboration, and you can organise everything in the project to subfolders and event sheets to keep track of things.
I'd warn you that it'd be best to wait until C2 is a bit more developed and its stability better proven before you go off making huge games. For example, large games definitely need a layout-by-layout loading system, and right now C2 loads the entire game before running. We're going to fix that though, so in a few months it should be a reliable, fast engine for big games :)