Randy (and all),
This may help.
Keep in mind that today manufactures have to bring to production, bikes that are going to allow them to be competitive in their sport.
In order to do this, the nature and design of the technology is no longer one that will suit the recreational rider AND the pro racer. In other words, you purchased a full-on race bike, (not an XR or some old TT).
And unlike bikes of the past, today’s bikes are meant to take on one to two motos and then be brought in for some attention - just as I would assume you'll see at any dirt or road racing event via the factory teams and advanced privateers.
In other words, with today's arena, you cannot design a bike to be competitive and also be low
maintenance.
In addition to this, it's expected that technology this advanced is also going to have its share of quirks. Things will fail, and things will break. Common place for everything from F-16 fighter jets to the top of the line Ferraris. And the harder you push them, the more you can expect them to fail. That's why nearly all top racers have full time mechanics.
As for the issues you see posted on this forum, don't jump to any conclusion until you have the full story.
For example, unlike older or recreational bikes, the rear suspension bearings and bushings on these things don't appear to be designed to hold a lot of grease. They do appear, however, to be designed to be taken apart and cleaned often, and lubed with a small amount of low duty grease. As one would expect from a bike designed to be nothing but competitive. And I doubt Yamaha has used Vaseline, but perhaps a mild grease that appears to look like Vaseline.
As for gear box and clutch failures, perhaps we would want to fully understand the circumstances and conditions that surround these cases before we form a mob and go after Yamaha. Yes, some of the clutch baskets may be too weak for those that work the clutch really hard. In these cases, talk gently with Yamaha about your issues or upgrade to a clutch more suited to your riding style.
Lastly, I don't think I have seen a Supercross or Motocross track in any part of the world that requires a bike to go through 2 feet of water. Again, not a bike designed for all things for all people so don't expect it.
If you find something in the design that you don't like, then modify it to suit your needs, (I hang out with guys that race Vipers and Ferraris that constantly have to do this...not to mention replace clutches all the time). If you think you have to modify too many things, or expect lower maintenance, then perhaps you did purchase the wrong bike.
Lastly, 5 to 6k for a bike that puts out this level of performance is actually a great price, even with the occasional gear, clutch, and hub failure. In looking at what it has taken Cannondale to build theirs, I can't imagine that the 400/426 was a walk-in-the-park for Yamaha either, ($$$).
The bottom line is this. After many years in motorsports, I have learned that failures and design flaws are part of the business. How you deal with these issues (this includes diplomacy) is really what separates the amateurs from the pros, and the amount of riding time we get in.
Best of luck.
Dave