It repurposes the class attribute to act like a pseudo-CSS ruleset with custom rules. To me that’s just ugly.
It does all its work client-side. For some things that’s a nice touch, but for a blog with mostly static content it’s wasted time.
It’s LGPLv3. I prefer less restrictive licenses for OSS.
On the other hand, I know the Pygments syntax highlighter pretty well, and I already had a written style plugin for it to get the syntax coloring I like. But there’s no mature Pygments plugin for WordPress that I could find. So I did what any good programmer would do and set out to write my own. I have the working knowledge of PHP (I’m a core dev, for mercy’s sake) and Python to do it with, after all. Not so much WordPress’ plugin API, though, so I took the SyntaxHighlighter plugin as a starting point.