I am totally on your side on this and I couldn't agree more to your point of you.
One of the reasons I've decided to start coding from scratch again was exactly this: Too many requests were made to customize the system resulting a complicated application, with many settings, confusing novice users and cluttering the whole idea.
My decision was clear. A GTD workflow injected into the system will prevent misunderstanding of its use, although most of the main features will be preserved.
Of course many new features will be introduced, mainly because I think they will greatly improve the usability of the application and were requested by many users: Reference items, Multi-step actions, on-the-fly sorting, exporting and printing will significantly increase the application's power.
The only drawback is more time on developing!
Starting with the first alpha release I hope I will receive user's feedback in a constructive way.
Thank you for sharing your point of view