I'll save you some time and money...
1) If there's exhaust that looks and sounds good to you, and it's worth the money to you for the looks and sound, then get it.
2) If you want smoother throttle control at partial throttle (e.g., initiating acceleration into a turn) and its worth about $300 and some loss of fuel mileage to you, then get a Power Commander.
3) If you want something more perfect for your bike than the freely available Power Commander maps, and its worth another $200-300 to you, then get a custom dyno tune.
4) If you really just like tweaking stuff on your own and experimenting with balance between throttle smoothness and fuel economy for exactly how you ride, and it's worth another $200 to you (and you're able/willing to learn how to use it properly, understand air/fuel ratios, etc.), then get the AutoTune module for the Power Commander.
5) If you're super geeky and not afraid to splice lots of wires on the bike, consider the Motty AFR Tuner. It's similar to the Power Commander + AutoTune, but also includes a data logger (Power Commander requires additional modules for data logging) and the ability to setup a switch to choose between two different self-tuning maps (Power Commander can use a switch to choose between two different static fuel maps, but when the AutoTune is plugged in, that switch becomes an on/off switch for the AutoTune feature). But it's not plug-and-play like the Power Commander.
6) If you choose any of #3-#5 above, you might as well do this free/simple air box mod:
https://www.fjrforum.com/forum//index.php?showtopic=105719. No one has done a before/after dyno run yet, but it seems logical that it might give a bit of extra performance. Worst case scenario: buy a new air box for ~$30 and return to stock.
7) If you want a noticeable increase in overall performance, get a full suspension upgrade.
8) If you really want a significant overall gain in engine performance, then trade the FJR for a ZX14 or Hayabusa and spend extra money on making it more touring friendly. Or maybe even a C14 with the secondary butterflies removed, full Area P exhaust and Power Commander.
The setup I've settled on is slip-on exhaust (Remus Hexacone, although there's probably no significant performance difference between any of the options out there), the "cdog" air box mod, and a custom tune (via a Motty AFR Tuner, although a custom map on a Power Commander would be just as effective). I think there's some performance gains there, but the smoother throttle and the change in looks/sound are what I actually experience and enjoy every time I ride it. If I could do it all again, I would skip straight to the setup I have now, and instead of experimenting with the Holeshot header (the primary suspect for
wreaking havok on my torque curve), I would put that money toward suspension instead. That's what I'm saving up for now.
The only reason I think there's performance gains is because I've improved my 1/4 mile time at the drag strip (from low 11's to high 10's). How much of that was due to me getting more practice at launching? Or differences in temperature, humidity, wind conditions? I have no idea. One of these days, I need to get my bike back on a dyno to find out for sure.