I've got a 2006 FJR and a 2011 Ninja 1000. I am specifically purchased the Ninja because I wanted something lighter which will still haul @ss and gear in a comfy manner. The main difference is wind protection (FJR is better). Minor issue is pegs on the Ninja are higher up and JFR has better lighting.
The range on the bikes are about the same (~225 miles).
Chain maintenance is required but it's not that bad. At home I've got a rear stand that takes seconds to get the rear wheel off the ground and spritz with Motorex 611 to clean it every 500 miles. Then every 1500 I apply lube. When touring I carry a Quik-Stand (
https://www.motorcycleradar.com/quick_stand.htm) (out of stock but there are similar ones) and after a long day (or every other short one) I use it and squirt some stuff on it. I've had a Scott-Oiler on previous bikes and they just make a mess and add unneeded complexity. You will need to budget for a new chain every 10-15k and new sprockets every 30-40k.
Otherwise, the Ninja will walk away from the FJR in handling and acceleration. If you think the FJR has effortless power, the Ninja has more. Some days I even wonder why it has gers 1,3,4,5 ... it's so tractable at all RPM's I can putz around town in 6th without lugging it and have plenty of acceleration available.
One complaint I have is that the gears are too close together and cruising RPM is higher than I'd prefer, so when I change sprockets I'll go +1/-2 ... already have a taller tire (195/55 vs 190/50) in back and that helps a little.
I have no complaints about the power but if I did, that could be remedied with Ivan's ECU reflash, PC-V and aftermarket exhaust; IIRC that will add 26 hp to the already stout 122 hp.
Hard luggage is available, sidecases OR topcase. Although it is possible to hack a solution for both at the same time. But I think the FJR's luggage is better.
Suspension is good enough to not have to replace it. The rear shock is rebuildable for about $350 (includes new spring and custom valving) at Traxxion.
I hear the FZ1 is a great bike too, and they can be found used for very good prices. A friend I ride with picked up a 2001 for $3k, already had Ivan's Jet Kit, some aftermarket can, gold valves, 20k miles on it. This thing supposedly puts down 150hp ... I've not ridden it yet. He is a conservative rider and in two years has yet to hit redline; says 7k is already too damn fast.
Ninja wins the performance side, FJR wins on arriving relaxed. Both can cover lots of miles with enough luggage capacity to allow for camping and have fun in the curves.