Just updated the PCIII to include the AP option.
It is a very suttle difference. It is only noticed when you are at Zero throttle and then crank it on. I think Jeff said it well.
The AP program is tough to "feel" in the bike, but you can definitely hear the difference in the drive train lash when nailing the throttle in the 3,000-4,000 rpm range. There is a noticeable decrease in the back-and-forth lash. You only hear one "nail" of the drive train.
The pdf manual suggests two options for Sensativity/Cycles/Fuel - 75/15/20 (Sport) or 90/20/15 (Street). I think the first question when trying different settings is to get the fuel amount right first. I tried the 75/15/20 first and thought it felt a little rich, tried the 90/20/15 and it felt better. So I just tweeked it down to 85/20/10. It doesn't mean that this is the "right" number. I only ran 4 tests. I think the goal of the AP option should be to smooth the transition from 0 throttle to throttle on, without making it more rich than necessary. With this respect the AP option, while a small difference, is a step in the right direction.
I briefly tried the PCIII with no AP, and was impressed with how good the base level map is w/o the AP option. I love the PCIII.
Four adjustments and test drives around the block in only 40 minutes. I couldn't do that with a carb. Nor would I have the level of adjustability that you have with this product.