Other than the more 'advanced' GUI from Java mission control, how are they different?
At first glance they seem to offer very similar functionality (Interpreting JMX data and Memory/CPU profiling).
However, as they are both shipped with the JDK (I'm using JDK 1.7.0_51 SE) I'm assuming there are significant differences, otherwise they would be combined into a single solution. Especially as this increases the size of the JDK significantly.
Is Java Mission Control ultimately going to replace JVisualVM in the future?
One important point is that Mission Control is potentially not free to use on production environments. It is free for applications running in DEV & QA and Oracle are not currently enforcing the charges for production applications (as of Nov 2014). However, their executives have made it clear this may change in time.