This is an oversimplification, but IS and ES are still different and separate. In 6.0 they are more seamlessly tied together. For example, doc definitions in one environment are automatically replicated to the other. IS is a “full” broker client (no more B-E bridge/package). The ES adapters are being moved to the IS environment.
If you’re looking for reasons to pick WebSphere MQ (formerly MQSeries) instead of or in addition to wM ES, the primary reason I’ve seen companies use is that they’ve selected MQ as company-wide communication standard or it was already in place. wM has an MQ adapter. Unless there is a specific need/reason, you can work just fine with wM only.