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The problem is not that it is misused. The problem is that there is a small subset of problems for which it works passably (like many other technologies) and a large universe of problems for which it will cause you massive pain.

Using compiled XSLT-translets in Java (XSLTC) has a huge impact on performance, with transformations taking 0.5s the problem seems to be in the way your XSLT is written and pushing or pulling the data, not XSLT itself: http://xalan.apache.org/old/xalan-j/xsltc_usage.html

Compiled XSLT stylesheets must be very efficient; they're automata, like regular expressions.