It really depend. Speaking for Kubota engines, the fuel consumption is basically a wash. It takes more fuel to burn the DPF, however, the addition of electronic engine control and tighter tolerances create a more fuel efficient engine. Again, in the end, basically even. On most models, the addition of the electric components (engine ECU) for the common rail engine allow the unit to improve its torque curve and make some adjustments to itself based on varying conditions like load and engine temperature. It also allows for more accurate monitoring of the engine parameters like temperature, rpm, etc. I am not saying any of this in necessary worth the cost, but it is a benefit, not matter how small.
The major con is the price. Some people site the additional electronics on board (as a con), but we (the entire industry) have had electronics on tractors for decades and have had very little problems with them holding up in the "real world". In fact, most "electronic" issues have been caused by poor planning on the part of the manufacturer, not an issue with the electronics themselves. Or at least that has been my experience.
I hope this helps give you a little bit more info. Enjoy!