Using Makefiles as a backend from the IDE sounds good, but it was a nightmare in practice (we did it in the original versions of Arduino). Especially on Windows, it was impossible to get working consistently - some machines seemed to want / as the path separator, some wanted \ and some wanted \. We had to maintain multiple slightly different makefile version.
It was also difficult for people to make changes to the build process, because they'd get thrown by the common Makefile problem (like using spaces instead of tabs, etc.) Now, with the preferences file, there aren't many things you can change, but they are relatively easy. We could just pass all the variables on to the makefiles, but at this point there are some decisions being made that we be a pain to replicate in makefiles.
I kind of like the idea that the IDE does it's own thing, but we also provide a Makefile for people who want one.
It would be good to have a better way to generate function prototypes, but it's also a hassle to include another program, and so far, the current method seems to be "good enough".
Of course, these are all interesting ideas, and I appreciate the discussion.