Collisions

Why XML is Almost Perfect

Flexibility vs. Reliability The separation between validating and non-validating parsers gave XML enormous flexibility. However, it also makes it difficult to ensure that the same document is read the same way - consistently.
Parts is Parts While separating content from style is a good idea, we have lots of files floating around that reference each other sporadically. There is no coherent whole, just a lot of files.
Coordination Issues As long as developers stick to simple projects, or have control over all creators and recipients of information, most of these problems won't emerge. Once we start sharing complex information, they start to look ugly.