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You have to bear in mind that almost all programs suck, period, just like everything else. Poor programmers are not unique to Java. (when I was attending my university, in fact, most of the programming atrocities I saw from other people were in Visual Basic or C++, even though I primarily used Java for the last few years)
It's also pretty widely known that Microsoft's JVM is nonstandard. In fact, due to a court decision from a few years back, they're no longer allowed to distribute it.. but, of course, it still comes bundled with operating systems that were released before the decision. Some people still develop for it, but there's not much that can be done about that except to wait for those operating systems to fall into obscurity. Applets and applications developed using Sun's standard VM should run on any platform.
If the DS did have its own JVM, though, running cross-platform desktop applications on it would probably not be viable anyway due to hardware limitations. I, for one, would be interested in it simply for the virtues of being able to develop in a Java environment, so as to take advantage of some of the language's more powerful features, such as interfaces, abstract objects, and garbage collection.
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