I had the same choice to make and went with the '09 AE... and the auto-clutch was the decider. I'm not worried about depreciation. Everything depreciates, but I tend to own vehicles for a decade or so, and by that point whether it was an '09 or a '12 doesn't matter. With taxes, registration, etc., I'm at just over $14k out the door, and paid $11.7k for the bike itself.
Yes, I could have beat the local dealer out of a few hundred more, but the guy has to make a living, and if you want local dealers they have to be profitable so they can stay in business. I've been on the other side of this kind of deal, and it just isn't worth it to me to beat up the dealer.
I'm also 5'6" with a 29" inseam, and find I have to be on my toes with the factory seat in the low position, but it works okay. I had been torn between the FJR and the S10, but the Tenere is just too tall. Maybe someday someone will make a liter-class adventure tourer with shaft drive and a 30" seat height.
I'll pick it up either this weekend or next, and I'm looking forward to some multi-state trips later this summer.