I think you're right about it being somewhat overblown, but, there is SOME truth to it... it's just not 900 exclusive.
This type of charging system is the same type of charging system in your lawn mower, and for the same reason. Cheap, small, and light. I asked sfair once (the resident expert on the issue) and he re-iterated what I always suspected, cheap, small, and light!
Mine failed at 15,000 miles on a bone stock bike. All I had was an airhawk seat cushion in it. Heck I hadn't even replaced the headlight bulb yet! NOTHING electrical had been done. I was able to (armed with knowledge of what to look for with some research) to find the cause of the failure on mine. It turns out, a tiny hole had worn in the insulation (with evidence of wear all around it) causing an arc and a short, burning up the stator. That's probably what kills most of these stators. (It's not likely that being a little bit over load, or that sort of thing, burns up the stator. It's bad for the bikes electrical system and could cause OTHER issues, but, it's not likely going to cause stator failure from what I understand. A short from bad wiring might, I suppose, but, the stator is always at 100% output, if you overload the charging system you'll just pop fuses and/or have a dead battery at the end of the day, the stator continues to work as hard as it would if you weren't running anything but the FI and the spark plugs!)
Look up the million mile Harley. It's the first known Harley to reach 1 million miles. 9 rebuilds, 3 new engines in that time frame. Oh, and 23 stators (in addition to probably a couple more replaced before they needed to be when he rebuilt and replaced engines!). That's an average of 45,000 miles per. I frequent a Honda forum and the guys riding the older Goldwings talk about swapping stators, and the guys with the higher mileage V-Twin Hondas are swapping stators. It's just not a long lasting design.
Now, why does the 900 get a bad rap about it? Because not a lot of people really put serious miles on their bike, and the 900's stator seems to fail a little earlier. It also seems to be pretty exclusive to the '06 and '07 models so there may have been a tiny defect that Kawasaki quietly fixed. I chalk that up to vibration. Sportbikes rev higher but they rev a little smoother being an inline engine, and don't often pile on the miles. 900's rev quite high for a V-Twin, and vibrate a bit more. It's a mild and 'high frequency' vibration that most people don't really notice until 75+mph, but, it's still there, and is probably faster/higher frequency than the bigger twins, so it has a better opportunity to vibrate and wear through the stator. The stator cannot move AT ALL, there is very little clearance between it and the rotor, so it is SOLIDLY mounted, on the OUTSIDE of the engine case. Er go, more and more vibration piled on.
But, anyway, my point is, the stator is the issue, not the 900. It's just a poor, outdated, unreliable design. (But I'm not an engineer, so perhaps there is no practical way to install a better charging system on a V-Twin motorcycle. What are ya gonna do, incorporate a serpentine belt and an alternator?) Look through this forum you'll see stator failures in all sorts of models. Google 'stator failure' and find all sorts of bikes dealing with it.
I kinda just chalk it up to the additional maintenance of owning a motorcycle. Clutches don't last as long, tires don't last as long, etc. I did it once at 15,000 miles, cost me about 200 bucks, even if I had to do it again at 30,000 miles (though it doesn't sound likely, the Rick's stators are supposed to last longer. They have a much thicker and MUCH harder insulation, so I bet that's why), I still wouldn't be unhappy with my bike. I didn't pay much for the bike, it's done fantastic, and is a great ride. I'd rather NOT pay that of course, but... well you get the idea. I suppose if I was paying $1,200 to have a dealer do it like some, it'd be a bigger deal.. but.. anyway...
Edit: I should also mention that mine is an '06, AND, I ride mostly 55mph +, that's just the way it is where I love, very rural, mostly county roads and state highways (or interstate). So I am in a perfect recipe for early stator failure, lots of CONSTANT SPEED riding (nearly all of it), combined with mine being from one of the two years that the vast overwhelming majority of 900 stator failures seem to be from. Dunno if it's age, or, perhaps a defect in the factory stators (maybe a weak spot in the insulation?)