I like what I have seen of Cypher, it looks very similar to XQuery. Neo justify it in their talks with "Developers don't get SparQL" which I find weird (as well as shocking) as Cypher looks similar to SParQL to me. The example where they were doing date comparisons by comparing date month and year suggests an impoverished type system. and there is also a potential pitfall with the ability to allocate properties to both nodes and relationships . If one is not careful how that is modelled you can suddenly find yourself effectively stuck with a schema that is cumbersome to unravel and you are nowhere near as agile as you thought you were.
Don't need an intermediate GraphML step, since Cypher looks so agreeable just generate it direct from the XML. In fact the quickest way to a graph would be to hack the original text files into Cypher's LoadCSV format. However the XML is still valuable as a source of denormalized master data so you won't need to pay the price of graph traversal to service such requirements.
So for now I press on with that as a dual solution. Neo looks a very good fit for this sort of application. Thank you.