I've test ridden my AE for about 8000 miles now, 6200 going to WFO and back. Some high speed slab and state highway, some switchbacks and tight stuff. High altitudes, wet roads, high temps, low temps (40's up on Mt. Evans).
The bike never missed a beat. I found that when things get tight, finger shifting was a plus. I haven't ridden the '06 as aggressively as my '04, but nearly so, and the shifting and responsiveness is pretty darn good.
Overall I think the '06 is a noticeable improvement over previous models in most respects. Contrary to other continued heat complaints, I think the '06 is one of the coolest motorcycles I have ever ridden, temperature-wise. The ergonomics are better, the bike feels lower and more stable. The stock suspension might be better, but still not as good as my Wilber-ized '04. That's probably why I wasn't as aggressive, especially when you throw in the unfamiliar territory I was riding in.
The shifting of the AE when cold is a bit grabby in first gear, but after a little riding and getting it completely warmed up it's smooth as butter, even in gravel at walking speed. I know this for a fact, after miles and miles of riding behind a "follow me" on construction gravel, especially in Wyoming.
There seems to be a lot more clunking going on during the foot shift versus the finger shift, but I really don't pay that much attention. The process is noisier than a manual hydraulic clutch, but the effect is about the same and the clutch dis/engages very smoothly. I think I have unconsciously learned to modulate the throttle to make the shifts smoother, similar to what we all do with a manual. And I can tell you that if you whack the throttle and shift at high rpm (or from a standing start), the clutch will hook up "with authority". I think in that regard that 99% of us would be very content with the way the electronic brain works the system.
At this point, using the electric shift is second nature to me. It's really a passive system once you get used to it, and it works very well. I still occassionally grab for the left lever, and probably always will. I think that Yamaha did a fantastic job on this first production run of the electronic shift. It could be improved and it surely isn't for everyone. But it is far more effective than just calling it a novelty, it just works too well. Will it replace a manual lever and toe shift? Seriously doubt it. Will it bring loads of people to purchase this model of bike? Seriously doubt that too. But I think it is everything I was hoping for when I ordered the bike last year, and Yamaha gets two thumbs up from me for their success in execution of the electronic shift on the FJR.