Bona fides, since I'm a newby here on this board:
I bought an '05 Ninja 500 new, from an L.A. dealer, using the "fax trick." (Fax the 10 nearest dealers to you, asking for a quote on the exact model you're interested in, saying you'll buy the best offer you get that day. Fax the best to the second-best offer, see if they'll beat it. If yes, try that once more. Go in and buy at the best price). I've got about 22k miles on it in two year's worth of riding. I ride 66 miles round-trip to work and back, five days a week. I live in L.A., so it rains maybe two weeks of the year, so I drive the car then.
I ride up the Angeles Crest Highway pretty regularly, full of blind corners and tight turns, and routinely stop at the bar halfway up the hill (Newcomb's Ranch). Met Jay Leno there once, he was driving a Porsche Carrera GT.
To the original poster- I think that the motorcycle market is heavily segmented, and each segment wants something different. So the EX500, although a 20-year-old design, remains a "sport bike." And people who buy sport bikes want sport. The engineering compromises all favor sport, so light weight (exotic, delicate materials) and high performance (exotic, delicate design) are all chosen instead of heavy weight (durable materials) and low performance (robust design, fault tolerance) designs.
While people who want cruisers want high mileage, low maintenance motorcycles. These engineering compromises require the opposite of sport, giving low performance (robust design, long-lasting parts) and heavy weight (easily worked metals instead of exotic plastics).
So cost calculations become really difficult, because a lot of desires are contradictory.
Personally, I set up my cost equation by adding in the amount of maintenance, value of my time, initial purchase cost, parts cost, insurance cost, and gas cost, then amortise it by subtracting expected residual value, and dividing the result by the number of months I'm expecting to keep the motorcycle.
Then I throw that number away, and think about how much I want the bike I'm looking at.
By doing this with different motorcycles, you can get a real feel for what your actual costs, per month, are like for each bike you're considering. The results can be surprising. For example, a 3-year-used Ninja 250 is so much cheaper than anything else you'll look at, if minimal cost is your sole goal, that's what you'll buy and replace, every two years (assuming the value of your time in maintenance isn't very big).
Not very exciting, though.
Whereas a BMW R1150R is more expensive per month (less than you'd think though!), but you can keep for 10 years, so your amortised cost isn't that much more.
But then you're stuck with the same bike for 10 years. Boring.
Personally, I'm (heathen! heretic!) seriously considering something like a BMW F800ST because to my mind, it's a good blend of performance, gas mileage, commuting practicality and ease-of-maintenance. But I haven't made up my mind yet. Might buy a Honda Interceptor (>gasp<) instead- valve adjustments are in 16k mile increments on them. Or (*choke*), the Harley Sportster just got an EFI system for '07... (heh) Or I might just pick up another Ninja 500, since I'm slowly getting used to the maintenance work- the first time I adjusted the valves on my current one, it took me about 6 hours to figure out what had be removed, and how to do it. The second time took about 4 hours. I'm hoping the next time will take closer to 3... guess I'll find out next month.
Cost alone is only a part of the total equation though, and because engineering is all about trade-offs, better defining what you want and expect will make sure you get a bike which better meets your needs. Sadly though, there's just no such thing as a perfect bike. Well, not until the one from Neal Stephenson's Snow Crash becomes a reality, anyway.