I had an 05 ST1300 for four years. I never felt that my ST was hot unless it was 105+ outside and lets face it 105+ is just hot period. My 05 was totaled in an accident earlier this year and like you I was itching for a change anyway so change I did. The stock seat on the ST1300 sucks big time. Stock seat on the FJR is tolerable, but nothing beats a good custom seat on any bike. The ST1300 is ridiculously smooth. The FJR is certainly better than the average sport bike by far, but you can't beat the ST for it's smoothness. On the flip side of that coin, the ST is so dang smooth that it's almost uninspiring at times. It did feel boring at times. The FJR never lets me forget the sport in the sport tourer.
I love the weight difference between the two. I didn't think I would notice it that much, but I do and the difference is big. On top of the 85 or so pounds the FJR is lacking, the FJR seems to carry it's weight down low compared to the ST which is another pleasant surprise. The FJR is certainly quicker, but... I can ride the snot out of either bike in the twisties so not a huge advantage either way for me. Both bikes are capable of running the twisties faster than I really need to be traveling anyway. Then again... twisting the throttle on the FJR brings out a larger smile on my face than the ST ever did. The ST is a torque monster down low compared to the FJR. Honestly I think the difference is simply a matter of what you get used to riding. Both bikes will pull like a freight train, but you need to keep the RPMs up a little higher on the FJR. No biggy.
Drop the ST and the damage is very minimal to say the least. The FJR not so much. However, when the ST1300 starts to go over you better get out of the way because you're not going to catch it. When the FJR starts to go over because you forgot the dang kickstand, you have a good chance of saving it. I've already experienced that one on the FJR and I had no problem pulling it back up before it went all the way to the ground. Try saving the ST from a similar drop and you'll end up with strained muscles and you still have to pick it up off the ground. The ST1300 also has more storage room over all. The saddle bags on the ST allowed me to carry more, but with the Shad top case I added to the FJR it's not an issue for me.
There is a lot I like about both bikes. Plus and minuses on both sides. Part of it is personal preference and part of it is getting comfortable with whatever you choose to ride. If you've got the itch for a change and you don't mind that slight in-line four buzz with a sporty moto exhaust note and you want something that weighs less than a small land yacht, the FJR is a sweet ride for sure.
