I have worked with xsd.exe before, and have had my share of complaints with it.  Although it is a powerful tool, you are also at the mercy of what it wants to create, and often it's just not what you want.  Nothing like generating a bunch of public fields  :)

Peli posts a link to a new app XsdTidy which seems like it may be a nice flexible replacement to xsd.exe.  I had thought of coding this myself after seeing this, but of course never actually sat down to do it.  Glad I didn't.  I hope to check this out tonight.