The Arduino and Freeduino use a FT232R as a way of connecting the microcontroller to the USB bus. The list price of the FT232R is about USD 4.50 in small amounts and is quite expensive compared to the other parts.
Would it be worthwhile to do a redesign of the Freeduino board and use a Prolific PL-2303 (about USD 2.80 in small numbers) instead of the FTDI part ?
It must use different drivers than the FT232R, so I’d say no… not worth it.
The FTDI chips have far better support across different OSes. And it just works. Are you really at the point where you need to save $1.70? 
Not that I am a huge arduino fan, but if I was going to break compatibility on the hardware, I would go for a new uC that has integrated USB and more power/features to boot, such as an LPC1751. The cost would be lower too ($5.33 for the 1751 vs $4.30 + $4.50 for mega328 + FT232R). Just something to think about.
Thats basically the approach the LeafLabs people are trying, with the STM32.