It would be nice if the VCCIO of the Mini USB could be selected in a way like described here in the FTDI datasheet on page 22.
I've made a little low-power Arduino-compatible setup with an ATmega8L running on 3.3V. I can't program it "in-circuit" because of the logic level difference (I'm putting it in a breadboard on 5V all the time to program it). The FT232R has a logic level translator built-in, so why not make use of it?