I've seen suggestions that an IDE should be added to FME Desktop. Sounds awful. More stuff that can break and in need of updates.
I do agree, however, that there is a need for better handling of scripts. So why not allowing the PythonCaller, and the startup and shutdown scripting features, as well as any future scripting features, to load external files? Yes, I know you can load external files as modules, but you still need to write a script in one of FME's editors for scripts to do so, and these are unaware of typos and such, as far as I know, that is.
I see before my eyes, a simple button that opens a dialog box in either of the current editors, a dialog box from which you could point to the external Python file and that would solve a whole lot. Then you would be able to write a script in your favorite IDE, have FME load the file and run it, edit the script some more, and have FME rerun the workbench, and you would never have to worry about syntax errors and such things (provided your IDE supports dealing with those).