The short answer is “don’t worry about it”. It sounds like the underlying concern here is project layout and the best answer is to keep your projects in the exploded WAR format that MyEclipse has liked since day one. This format is going to be compatible with every IDE out there and is easy to import/export and reuse even from the command line.
The flexi project support we were gunning for in WTP was not implemented in a fashion we were hoping for, for the immediate future we will be keepnig our project structure and connectors. Moving forward as WTP matures we will replace portions of MyEclipse as it makes sense. The “makes sense” part is hard to predict, each major update to WTP we evaluate and see where the major features stand. If it’s going to be a nightmare to pull them in or create a complete PIA for our users to transition over all their projects, we will ignore it until a better solution presents itself.
Trust us, we don’t like writing code for the sake of code. If WTP is doing something better than us, we’ll take it in a heart beat, that frees us up to do designers or other cool tools.