Hi Anthony! There's roughly TWO types of exhausts for these bikes with different results:
2-2 exhaust - stock pre-gen, tends to favour high-end flow and power, gutless down low
2-1 exhaust- stock new-gen, favours low-end/mid-range flow and torque, not as much high-end HP
In order to buid either one of these, pipe-diameters, lengths and other physical properties must be optimized from beginning. You simply cannot convert from one to other. It must be built with one or other design in mind when tubing is selected.
If you compare new-gen 2-1 exhaust, you'll notice that pipe-size after 2-1 merge is significantly larger than 2-2 exhaust. And muffler needs to be twice as big as well to flow twice as much exhaust. For pre-gen, which has reputation for being high-RPM screamer with not much down low, it's best to get 2-1 exhaust for low-end/mid-range improvement. Much, much more useful for daily-driving.
I've got some photos and measurements comparing them here:
an Exhausting Tale!!!
Area-P's 2-1 pre-gen exhaust and development process:
Official Area-P Pre-08 Ninja 250 Exhaust Thread