Hey, we're listening.
There's no great reason why Arduino currently uses uisp instead of avrdude. That's what we got working first, we haven't had any complaints about it (until now), and we've been too busy fixing other more important things to worry about it.
We may look at switching to avrdude soon. It definitely has some advantages (e.g. supporting stk500-2). The use of a configuration file instead of command line options makes it a little more difficult to invoke from another program, however.
I'm going to try to incorporate a menu item for burning the bootloader into the IDE. Maybe I'll use that as a chance to try out avrdude.