Some of the performance difference is related to the driver model implemented in Mesa, but the work being done on Gallium (as a replacement for the current Mesa HW driver model) will go a long way to fixing those issues.
The other big issue is that the underlying support code (drm, memory management etc..) is quite a bit "older" in design and functionality than what we use in the binary drivers. Again, the good news is that this is being addressed today. Between the addition of memory management to the kernel (drm) and the work being done to refactor command submission and fencing in the drm, there should be a big lurch forward in both performance and stability over the next 6-12 months.
The lack of good memory management has also been a factor for the degree of OpenGL support (extensions etc..). Again, once memory management makes it into the kernel I think you will see a lot more progress being made in terms of level of GL support.


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