To me, who has only basic understanding of modern engine ecu tuning, what seems extremely complicated, once broken down into its component parts really is just a series of logic steps controlled by sensors. Whilst I have had 4 engines tuned using dynos to optimise the AFR and power/torque curves (doing research before hand to see what exhaust systems result in the most linear responses), I have also tuned many carburreted bikes myself, as well as whole engine rebuilds.
What has been immensely useful in this thread is the very logical breakdown of the principles behind how the ECU works (thank you Roger 04 RT for your very informative posts). As was said, the principles really are little different to carburetted bikes. More power = more air and more fuel with the ability to use that mixture efficiently and with engine life, smooth running and reliability factored in. The limit is reached by the amount of fuel that can be burnt efficiently, dictated by engine displacement, cam profiles (hence volumetric flow capacity of valve open durations), compression ratio, revolutions limits, ignition efficiency and things like exhaust design for best gas-flow and back-pressure.
BMW have obviously optimised running for their bikes for engine longevity with a sensible margin on reliability, so really (and especially looking at what the bike is) wanting significant power increases, one is better to look at an alternative bike that gives that from stock. It's often cheaper to buy a bike with more power as standard in the first place than to buy one with less power and tune it, so really where the big old GS1200 is concerned, most people recognise that and are really looking for improvements in drivability through the strangled emissions control areas where the bike is designed to run leaner and more efficiently.
I've only ridden a handful of WC GS1200 bikes, including my own and each one has felt slightly different. My current GSA is most definitely the smoothest one I've ridden (hence part of the reason I bought it) and doesn't seem to have any trouble pulling 6th from 45 to 50mph cleanly, and will pull hard all the way to the red line without any obvious significant dips. There is a very slight flat spot between 4,000 and 5,000 revs but it soon pulls through that and rockets away. I haven't noted any on-off lumpy fuelling at low revs save in dynamic mode. Then, filtering in 1st gear through traffic isn't the way to go as it can be a little jerky with the near instantaneous response but left on standard road mode and its fine. I'm unsure though of how typical my bike is of the breed as a whole, but if this does sound familiar, then I'd question really why anyone feels the need to go to the cost and trouble for really very small benefits. AF-XIED does seem a pretty good compromise to those just wanting to eliminate the 4 to 5K flat spot but for me, it pulls so quickly through that I'm not bothered personally. I may give the AF-XIED solution a go down the line but for now just enjoy riding the thing as it is. Standard.