I chose to go with the Yamaha Top Box when I got my '04, I like it, its handy and serves as a comfortable backrest for pillions. Never any complaints. Many here think the Yam model is ugly and too small. And some think both the Givi and the Yam are positioned too far forward.
You will never turn the FJR into the comfort tourer of the Goldwing for two up riding, but there are many on the forum who ride long hauls two up in comfort.
As for the '06? I expect Givi is close to having their rack and colours ready for the '06s, as well as Shad and others.
Once you decide, post up some pics and share with us.