I have owned a 2005 Honda ST 1300 for four years and 16,000 trouble-free miles. The Honda, within the sport-touring segment, falls towards the touring side of the spectrum. The FJR lies towards the sport-side of the class. The handling and braking of the ST are decent for a bike with a wet weight of 710 pounds. The engine is extremely smooth, fairly tourqey, and gets good gas mileage. The gas tank capacity is 7.66 gallons with a range typically exceeding 300 miles. The wind-protection of the Honda is easily better than any bike in this class with the possible exception of the BMW RT. Overall, the bike is very refined and is an excellent mile cruncher. At the end of a 450 mile, 8 hour day, I feel reasonably good...On other machines I have become, after that number of hours and miles, irritated with some issue(s). This isn't the case on the ST 13.
Motorcycle Consumer News, probably the most objective motorcycle magazine published in the United States, and supported entirely by subscription fees as opposed to manufacturer advertising dollars, tested the C14, ST13, and the FJ13 in their December 2007 issue. The FJ narrowly beat the ST13; the C14 finished last. I believe Bike ranked, during a similar comparison, the ST13 first.
Based on my test ride of a 2005 FJR, the bike handles and accelerates better than the ST13. However, the engine vibrated, the brakes were mediocre, and the throttle was stiff.
My advice is to identify/prioritize what you really want from these bikes, how you are really going to ride, and then test-ride them for a decent amount of time and miles to make your own decision.