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From briefly skimming the MRPT website it looks like they're trying to provide a toolkit that helps with many of the common things you'd like to have mobile robots do. Part of what they're providing is a way to have a mobile robot navigate through the world much like the ROS navigation stack. It doesn't look like they have support for ROS yet, though they are working on it, but once they do MRPT will provide another option for running ROS-based navigation on mobile platforms. Which approach to use will likely depend on your specific application and preferences, I'm not sure there'll be a great rule of when to use one over the other.
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