Indeed the XmlSerializer implementation of .Net Compact Framework 2.0 and 3.5 differs. The solution to this "new" behaviour is easy as well. Because the XmlSerializer which - in my case - serializes XML as a "fragment", we need to declare the XmlRootAttribute. This is due to missing XmlRootAttribute annotation of the type to be serialized within the Reference.cs. To be backward compatible with XML serialized by NETCF 2.0 implementation, we need to add the namespace by definition of InstallDirective (Reference.cs). Unfortunately I found no programmatically way to get this.
Before:
XmlSerializer xmlSerializer = new XmlSerializer(typeof(InstallDirective));
FileStream file = File.Create(@"\tmp\install\funnyInstallDirective.xml");
TextWriter writer = new StreamWriter(file);
xmlSerializer.Serialize(writer, installDirective);
After:
XmlRootAttribute att = new XmlRootAttribute(typeof(InstallDirective).Name);
att.Namespace = "java:my.foreign.namespace";
XmlSerializer xmlSerializer = new XmlSerializer(typeof(InstallDirective), att);
FileStream file = File.Create(@"\tmp\install\funnyInstallDirective.xml");
TextWriter writer = new StreamWriter(file);
xmlSerializer.Serialize(writer, installDirective);
Credits to ta.speot.is who answered the question here.
[UPDATE] Of course you can beautify it by using the annotated XmlTypeAttribute of the web service type. It will look this way.
XmlTypeAttribute ta = (XmlTypeAttribute)Attribute.GetCustomAttribute(typeof(InstallDirective), typeof(XmlTypeAttribute));
XmlRootAttribute att = new XmlRootAttribute(typeof(InstallDirective).Name);
att.Namespace = ta.Namespace;
XmlSerializer xmlSerializer = new XmlSerializer(typeof(InstallDirective), att);