Having owned two FJR AEs, and a K1600GTL, I have to tell you that the FJR holds its own against the K1600. I re-bought the second FJR after having owned the K1600 for about 5 weeks and I will keep both.
The K1600 shines for situations where you need a lot of storage space, and it also shines if you're too lazy to check your oil or your tire pressure the conventional ways, or if you're too lazy to dial in your suspension by conventional methods. And the factory cruise control, is very nice too.
Otherwise, the K1600 has a lot of weight, and the guys who tell you that it evaporates once your underway have forgotten that you do have to slow down again. I like, maybe even love, both of these bikes, but if all you've got is an FJR, you could do a heck of a lot worse. The FJR is a great bike, and with over $15,000 less invested in my current "new leftover '09" FJR compared to my "new '12 K1600," you'd have to put an awfully large premium on the gadgets, extra storage space, and sexy 6, to justify the extra money.
As for an FJR upgrade, I don't see it coming. But if it were being considered, I wouldn't mind factory cruise, electronic tire pressure and oil level monitoring, and saddlebags that were large enough to stow an XL helmet. Aside from these upgrades, I can't think of a thing.
Go out and enjoy your FJR!