Thanks Guys. I was convinced that going back to a 25 hp 2-stroke was the the right motor of the boat. A real advantage for the 4-stroke I appreciate is I can use the same gas in my larger boat and my generators. I was intrigued by the option of getting ~25 hp out of the 15 Suzuki. For most of the 4 strokes the 9.9, 15 and 20 are all the same motor, when you jump to a 25 it's in a different family. The 25 4 stroke is about 40 lbs heavier than the 15 which could be a real advantage.
I chatted with the owner of the business. The reprogramming only pushes the motor ~ 5 hp beyond is it's design. He said that the original programming of the ECM has to work across a variety of fuel grades and to get the extra HP from the motor the programming is optimized for higher octane fuels (93 Octane). I'm not sure why it would cost so much to refresh the drive, apparently it takes only a few minutes. It seems like a good option, but as Eric says, a used 25 is proven and might be cheaper.