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The biggest practical problem at the moment is lack of support.
The computer algebra documentation is not very Muggle-friendly.
Somebody needs to write a nice tutorial that covers the tiny
subset of features that is needed in an introductory course.
This includes documenting how to avoid the usual neophyte
mistakes (such as expecting the system to be more capable
than it actually is).
Some pros and cons:
-- quickmath is free but very limited, for instance when it
comes to chaining together a long calculation, AFAICT.