I currently own and ride an 05 ST1300 (20k miles or so) and a 05 Yamaha FZ6 (5k miles or so). Never rode an FJR, just sat on them. With that said...
I purchased my 05 ST1300 in Feb 2005. At that time, 2 of the big reason I did not get the FJR was the heat issue supposedly being worse on the FJR than the ST and the valve ticking issues some FJR owners experienced. Coming from an '02 BMW 1150RT, the last thing I wanted was yet another bike that I had to worry about mechanically. The ST1300, from all accounts and so far in my experience, was/is very very solid mechanically. Again, coming from the 1150RT with "soul", the idea of having a solid dependable bike like the ST1300 was very appealing.
Since it was going to be my everyday ride and main source of transport, I was also concerned with weather protection. ST1300 seems to have the edge here.
How fast do you want to go? The ST1300's top speed is in the 150mph range, I'll never want to go that fast on the street, much less faster. Passing is a breeze as well, if done correctly.
For a big bike that is over 700lbs wet, the ST1300 handles pretty good...for a big heavy bike. That qualifier is why I ended up also getting the FZ6, which handles great and loves to eat up twisties. I wish the ST1300 wasn't quite so heavy, although it is balanced quite well with the V4 engine.
The ST1300 also has a more robust alternator than the FJR. At least it used to, anyone know if the 2006 FJR has a better Alt? It's nice not having to worry about draining the battery when adding on farkles, especially if you have any heated stuff or extra lights.
The riding position on the FJR is a little more aggressive than the ST1300. Although that can be adjusted with risers and other mods. I'm curious how easy it is to adjust the risers on the 06 FJR that has the built in 3-way adjustments?
The ST1300 engine growls quite nicely when hitting the throttle hard. The sound grows on you. I actually like quiet bikes, better on all day rides. I would never let how a bike sounded be a deciding factor, unless it was just way too loud. Can change the sound easily enough with pipes or slip-ons if you wanted.
I live in Tampa, Fl where it can get quite hot and muggy. Rode the ST1300 in 90F+ temps and 90%+ humidity many times. Was I hot? Of course! Drink plenty of fluids, air flow, evaporitive cooling, etc etc etc. So it is doable. That said...now that I have the FZ6, if it is dry and 70F or higher, I ride the Yamaha which is much cooler to ride in hot weather.
IMO, the ST1300 with bags looks better than the '05 FJR with bags. I never take the bags off, so could care less what they look like without bags. Not that the FJR looks bad, not at all, looks great with bags too. Just preferred how the ST1300 looked.
I have never, ever, never had a problem seeing the LCD on the dash. And I have ridden in all sorts of different lighting conditions. Maybe it is height dependent? I'm 6'2". Maybe it is 'cause I always wear sunglasses? I don't know, but I never did understand why people complained about the LCD brightness. I think at least a few of them didn't know you can adjust the brightness, it has 3 settings.
If you are coming from a cruiser V-Twin, then moving to a bike with a V-4 engine might be easier for you than to a bike with an Inline-4. Then again, maybe not...something to think about anyway.
You can wheelie the ST1300. Done a few power wheelies myself
Not like a sport bike of course. Truthfully though, if I lift the front wheel, I think of it as bad power management.
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So, now you are probably wondering why I am looking at this board if I have an ST1300 already? The new FJR1300A
E caught my eye. If that bike had been available when I was looking last February, I probably would have ended up on the FJR instead of the ST. Supposedly, the heat issues are resolved, as well as the ticking issues. If a used one crosses my path toward the end of '06 I may end up with one
Depending of course on real life user reviews of the bike once they hit the showrooms.
Getting the FZ6 has inflamed my handling desires. I would love a touring bike that handled great, without having to tag on "for a big bike."