I have not driven one of the MY09 common rail diesels as they have only just arrived in Australia this month and we will pick up my partner's Eos this saturday
It is my understanding the main differences are in engine technology rather than performance - the common rail units make it easier to achieve emission control requirements and also allow better fuel economy by using more precise control of fuel injection volumes. The possibility of remapping the electronics to achieve higher power/torque outputs will probably increase over the next year or so
Apparently, the big downside is that the current common-rail system is not suitable for bio-diesel other than a 5% bio blend, the VW fuel recommendations and warranty exclusions reflect this situation. I have not been able to find out why so far but speculation suggests it is related to the relatively greater "compressibility" of bio-diesel compared to mineral diesel meaning it is difficult to obtain optimum fuel/air ratios using the current common rail technology. I also suspect soot generation in city driving conditions clogging the standard DPF filter might also be a reason.
Perhaps I am naive but given the strong possibility of government-mandated bio-diesel fuels in the future; I would be surprised if VW would introduce technology that cannot be readily converted to bio-diesel in the immediate future.