I fully understand this. Maybe cmake is worth a try... Though cmake would add many more MBs.
I forgot one thing that's really great about using a makefile now:
You can have your preferences saved with the projects.
E.g. on some boards you prefer to use the bootloader while with others you're setup requires an AVRISP MKII - in any case you just set it once. Esp. ATmega8 vs. ATmega168 switching becomes obsolete! I guess some catch this problem often nowadays when having diecimila and older boards around at the same time. Also you can have different clock speeds and baudrates without changing preferences everytime you switch projects etc...
Yes, this is rather advanced stuff, but it's nice beeing still able to do it with a makefile - just as you said, david. I agree, as long as prototype creation works most of the time, better don't touch it...