I’ll add Business Problem or Context as another criteria. What is it that you are integrating?
If it is high level information such as PurchaseOrders that are produced by one system for the consumption of one or more other systems, then the IS is probably the more appropriate tool. What I am really trying to define is an integration with few types of information, relatively speaking few number of documents, and often single producers of documents with single consumers of documents.
If you are talking about integrating two or more systems internally in near realtime and in order to keep the systems in synch you need to exchange many different types of information of much smaller granularity with a much greater volume, then the Enterprise Server is more appropriate.
The only reason I think (note: CONJECTURE) the Enterprise Server might go away is if webMethods decides to get out of the Enterprise Application Integration at a systems level in favor of Enterprise Application Integration at a business level.