What to do?

Subsetting The subset approach lets you work with others using the smallest set of tools understood to walk across a variety of systems. Common XML, for instance, defines a 'core' of features guaranteed to work in non-validating parsers with or without namespace support. Minimal XML goes further, stripping the world down to elements and content.
Documentation You can just describe the needs of your XML documents, for people and machines. It's a safe strategy in that you can say 'I told you so', but not always reliable. XML Processing Description Language (XPDL) is one attempt at providing a machine- and human-readable version of such information, and the never-started packaging work noted by the XML Activity of the W3C might be another. Schemas don't carry this kind of information.
Redundancy Sometimes it's possible to duplicate effort and make things work. For instance, you can provide a default value for an attribute in both a DTD and a schema, figuring that one or the other will get used, and, if it's really important, you can put it in the internal DTD subset of every document that needs it... This doesn't work for tougher cases like XML Base or XInclude, however.
Pray for cleaner layering Consider everything XML-related from the W3C as experimental, figuring that they'll sort it out and come back for cleanup later.