Took a B12.5 out on a demo ride today so now I can compare the two back to back.
Keep in mind mine has a Muzzy full exhaust and holeshot stage 1 /w timing advancer.
Power
Below 3krpm mine has more grunt...sorry folks but it does.
4-6krpm the 12.5 gets the nod...significantly more acceleration
6krpm+ mine will walk, then run away from the 12.5
For day to day riding I'd give the 12.5 the advantage here...especially since that's the range I mostly ride in.
Throttle response
B12.5 good, my B12 awesome...the 12.5 is too snatchy at low revs compared to my carb setup. Cracking the throttle wide open (from any rpm) mine feels more responsive and is more linear than the FI. I give the 12 the advantage on throttle response (if jetted correctly)
Handling, seating, controls, ergos
Identical (remember the 06 has the same body/chassis/controls as the 07)...even though the B12.5 is heavier you really can't feel it in the handling but I think mine was slightly better under aggressive braking due to its lighter weight...you'd have to prove that with tape measures though.
Vibrations
B12.5...very little vibrations from the engine...it is smooth...hell the mirrors aren't even blurry. Nod to B12.5.
In the end the bikes are so similar that you'd be nitpicking to say one is better than the other. I like mine more just because of what I've done to it and am still ahead of the game for out of pocket expenses. BUT if I was to choose between a bone stock B12 or B12.5 I would go for the B12.5.
Then I took out a Busa...Busa's f#$&ing rock!!! More comfy, more power, better handling, better brakes...I couldn't believe what a fun bike the Busa is