Only you can answer that question....
As far as power demands and concerns about stator output, in reality, how often will you really have ALL your gear powered up? Pretty rare in my opinion, and installing a small digtal voltmeter can help you to cycle/manage your use. Bottom line is you have that post deployment spending itch..... LOL :yahoo:
So now that we have that cleared up... There are some real differences between 03 and other models. Body work, Brakes, Heat Management, Seat/Handlebars, AE trans, and a bunch of other options. Do those changes matter to you? For me they dont, I got exactly what I wanted. I prefer 90% of the Gen I 03-05 bodywork over the 06+, with the exception of the front hangover. I like the way the way the headlight/front of the Fairing looks on the Gen II, but prefer the rest of the Gen I body work. I also prefer the Gen I instrument cluster, and NON ABS. Everybody makes noise about heat management between generations, but I dont see that as a huge issue, and there are mods for anything if it is.
I cant imagine owning a Wing type ride till I am well into my 60's, and expect my 05FJR to be my main ride for the next 10-15 years. If I were you, I'd be looking at a hooligan type bike like a Speed Triple, FZ1, Monster, VMAX for solo blasting around, and making a few Touring mods to the FJR. THough there have definately been improvements, I dont think your Stator concern is a real world practical problem, or reason to move away from the 03.... But thats just my .02.