Great question that I don't know if I could ever answer. I am too much of a pragmatist about bike purchases to ever own a Ducati. Also, it is always form to suite the function. Obviously the newer Duc's perform better now and are more reliable than in the past due to new technology available today. That is expected That does not mean that it could not be simpler and better. I grew up loving Japanese work because of their respect for simplicity and performance. Ducati and BMW have always represented "other" and been priced beyond what I would be willing to pay and go to the hassle to have to find parts and get serviced. Perhaps if money was just a small issue with my bike budget I would have a few Ducatti in the stable but only if I could afford to have them serviced.
FWIW, my 1198 (which was also the only bike I've bought brand new and the one I've owned the longest out of my 5 bikes currently and previously owned) was the easiest one to work on. The ZX6R is not bad, the the 1198 was the easiest. I also had barely any knowledge of bikes at the time and that was pretty much the bike that I've learned a lot of the common stuff that I do now on all bikes, which is pretty much everything except tearing apart the engine and shock service, since that requires some special tooling. My little CBR500 which is supposed to be a "beginner bike" more or less, is a PITA to work on. I've had nothing but frustrating experiences while doing any work on it, compared to the ZX6R or especially my old 1198. So I kinda disagree about the japanese "simplicity".
As far as parts, yeah the OEM stuff is insanely expensive, but everything else is about the same unless you buy the aftermarket Ducati-branded stuff but Ohlins shocks for example cost you the same regardless of what bike it goes on. Used OEM parts can be even cheaper in a lot of cases. I've bought a gas tank for that bike in mint condition for $120 shipped. A swing arm also in great condition for $80. I sold my frame with clean title and no damage for $1000. I have yet to see those kind of prices for R6's or ZX6R's or GSXR's on the WERA forum or other popular bike forums. And those weren't just me getting the deal of the century. I had seen others that were similarly priced. The only thing that tends to go for more is the engine...but there's also a big difference in what you're getting so it makes sense. I sold my engine for $2500 with 6000 miles only. People are asking more than that for R1 or ZX10R engines. Not to mention the BMW or Aprilias...those guys are asking like $4000+ for an engine. Service as well....before I got rid of my Ducati, the local Ducati dealer was charging $95/hour for labor. The local Kawasaki/Honda/Yamaha/Suzuki/Polaris dealer was charging $125/hour. Not sure what they are now but I'm pretty sure the Ducati one is still cheaper.
My experience told me that the debate about the cost is more a myth that people like to exaggerate, usually those that haven't experienced it first hand. Sure the upfront cost is a bit more expensive. A 1299 is more expensive than the japanese bikes in that same class, but not by a huge amount. About 15-20% as far as msrp. Sure it's significant, but not like Ferrari vs a Honda Civic. Basically anyone that could afford to buy a japanese liter bike could likely afford to buy a Ducati as well. The main reason why the Japanese ones are cheaper is because their mainstream...simple case of supply and demand. Honda, Yamaha, etc. are pushing out at least 10 times more bikes out of their factories than Ducati does every year. Anything that you manufacture, no matter what the product is, if you're making and selling 10 times more than your competitor you can afford to sell for less.
Give it a try sometime. I bet you'll like them
...I was hooked on it when I went to a dealer to test-ride a used 2009 R1 and a 2009 1198. The guy at the dealer said "start with the R1. then come back and jump on the 1198 and see what you think". He didn't disappoint!