I have a 2007 AE and I feel conflicted about the auto clutch. ...
That said, sometimes I hate having it - especially because this bike's throttle is so abrupt and harsh. ..
I think the throttle was tamed in 2008, or at least it was on my 2008AE.
Both prices are high if you look nationally, but not bad for central Texas. I live in Austin and couldn't find an FJR at anything but list+ around here when I was shopping in late 2010. I wound up going to Tulsa and driving away a new 2008 Advanced Edition for $10500 OTD, and then payed sales tax here in Texas.
I really like the AE system myself, but many find its an acquired taste.
Before I bought my FJR I had a to test drive an ordinary FJR, and found that the high clutch effort was troublesome.
I also have a 29" inseam, and I think about lowering often, but haven't ever got around to doing it for the last 15,000 miles.