@jfheath has reported that he experiences less ignition knock with his 2009 vs his previous 2006(?). He has also reported having more torque available at very low RPM's. Both of these suggest different programming as a minimum.
To put some meat onto that. I had my 2006 from new, and I had a 2013 built A9 model from new.
The instant I got on the A9, it sounded 'raunchier'. A bit throaty, more of a noisy grunt. Not much more, but noticeable.
The A6 was much worse at climbing steep hairpins than my previous ST1100. I had to get my hand on the clutch lever before taking a very tight left hander. Forget counter steering, I'm talking about bends that you can only just get round. There was not enough power to drive the bike up the gradient and round the corner without slipping the clutch to keep the revs high enough to stop it from stalling.
By contrast, the A9 pulls up the same steep hill bends without having to worry about the clutch. It picks up the power from low down revs and just drives out of the bends. First gear stuff but the comparison is valid - a new ST1300A9 compared to an 70,000 mile 7 years old ST1300A6 - but the A6 had always behaved like that, and the engine was better at the end of my time with it than it was at the start - partly because I had balanced the starter valves, partly because the A6 pinked throughout its life when hot and when under heavy acceleration. Just a feint tinkling. The A9 has never pinked and there has never been any signe that the mixture is too lean.
In Summer, in Spain on high mountain passes, the engine would get too hot - it would reach a point where it sounded different as if the motor was tightening up and struggling - I thought with lubrication - as well as the pinking. I wondered if the oil was too thin at those temperatures. So we'd find a view and let it rest for a while. Then it was ok. Again, I was thinking 'too lean'
The A6 occasionally displayed an odd phenomenon. Usually not long after filling up - but not always. After cruising along without much throttle activity, a few times, I would aenter a bend or roundabout where I had slowed down, gone through the gears and relied on the power to lift me out of my lean out of the bend. It wasn't there. It wouldn't accelerate. I'd have to pull the clutch, blip the throttle a couple of times and then it seemed to wake up. A friend - who was high up in Honda UK and had lots of friends in the technical side - asked them about it. They told him that thye ECU changes engine modes accordding to how it is being used, and if you are coasting it takes a couple of throttle blips to make it wake up and switch into more responsive mode. Whether that is correct or not, I don't know, but I always blipped the throttle during slodown if I was wanting to pull away again.
The A9 has never done anything like that.
If I was to buy another, I wouldn't be buying one earlier than an 08 - mainly for those reasons.