Rich, where do I start? First off they are both superb motorcycles. Powerful, comfortable, capable with proven reliability. The ST has more than proven itself the equal to the FJR in eating up miles. But unfortunately Honda ignored it for years before finally discontinuing it. BTW they were working on a replacement and somewhere I have 2 pictures of a V4 prototype using the VFR 1200 engine however that never came to fruition. It was a nice looking bike and would have kept Honda in the game IMO.
The FJR has had the benefit of continual improvement by Momma Yamaha. The basic bike was already good and they've only made it better with the addition of a 6th gear, heated grips, cruise control, ABS, Traction control, slipper clutch, updated instrumentation, an electronic windshield that stayed in position when shut off, and an additional higher tech model with electronic suspension in the ES model that I don't have. etc. All stuff that the ST 1300 could have used if it were to stay competitive in the market place. The FJR's motor with 146 hp and 106 ft lbs of torque is a beast. It has always been considered the sportiest of the popular sport tourer's. That however has not been a benefit for me. I don't go thru curves on the FJR any faster or slower than I did on my ST. I'm not one of the more aggressive riders on either brand, I just ride...but I ride a lot. 300 days and 25,000 miles a year on average since I retired 5 years ago. You live in SW Ohio and you know the dedication it takes to ride 300 + days a year here. It's got to be accumulated snow or ice or an all day frog strangler when I wake up, to keep my bikes in the garage. I ride when it's above 100 and I ride when it's below zero. The ST has a lower center of gravity and lower seat height. Physically it was more comfortable for me with my stubby legs, particularly so with my seat cut down by Greatdaytoride.com. Something I am considering for the taller FJR, although the knee bend on the FJR is already tighter than it was on the ST with the seat lowered so it might not be an option. I have torn meniscus in both knees and don't want to aggravate those. I'm still pondering what to do to get me closer to the ground. There are options, but IMO there are no good options. So far I am managing, but know I'm just an iffy footing situation from another drop (which I never did on the ST in 10 years and 110,000 miles). The windshield range of motion was better on the ST and I've bought a taller shield for the FJR to make up for that. I've also bought another stock shield to cut down to get it lower in the summer (which I also did for the ST). I've moved my handlebars back into the closest position to me out of 3 on the FJR and they feel a little better, but the angle is wrong (too sharp of an angle), and the only way to fix that is with a $ 300 riser kit which also moves them up an inch and back an inch and a half and I'm not excited about that, feeling it would take away some of the FJR's sportiness. I never wanted risers on my ST either. I don't mind a little forward bend. Then again being so small, I'm sitting up against the tank on both anyway and not that far from the stock bars to begin with lol. The oil filter is way easier to change on the FJR...way easier and I like that. rear end oil change is the same. The FJR is 80# lighter than the ST but you only feel that when pushing the bike around by hand. Once moving I can't tell a difference. I think the ST's voodoo is the complicated linked braking system with SMC that seemingly only a few people in the world can properly work on and bleed. My local factory trained mechanics apparently couldn't and many members of this forum would have been in big trouble without the" white courtesy phone" apparently. Shame Honda chooses to over engineer things like that. Both have superb brakes, great handling and great powerbands, pulling tall gears from low rpms without complaint either single or riding double up. The FJR looks better without saddlebags than the ST did, but I rarely ride without them. . The ST holds a little more gas,but I get slightly better gas mileage on the FJR by about 5 miles per gallon. . The FJR uses regular. I always hated that the ST required premium. Stock seats I'd rate equally and neither bothered me. I can ride on both of them 10-12 hours a day.
It took me 34,000 miles before the ST became one of my all time favorite motorcycles, and I need a little more time (maybe another year) with the FJR before I am willing to make the same claim for it, but I will say it has potential. Liter class inline 4's have been my favorite motorcycle engine layout, ever since my first (KZ1000) in 1977, but I must admit the V4 of the ST 1300 was mighty sweet.
Does that cover it for you?