This is a quick dump. I will pretty it up soon.
From the beginning tools should be designed as a usable IDE (Integrated Development Environment) like Eclipse or NetBeans. Should be accessible to users with a variety of backgrounds. Tools (or subtools) should work together, seamlessly sharing a common representation for parts, devices, systems, and strains. New functionality should be easy to add via a plug-in interface, and should be able to take advantage of a common framework for displaying and manipulating DNA sequences, parts, devices, systems, and strains.