Jeff,
I was just thinking about this today and you beat me to posting it
Now that Joomla 3.x has tagging built-in, why not use native tagging (or extend it the way that other extend com_content), like this one has unified tagging across all of their site regardless of which extension they use?
I realize that this might not be possible at the moment (as the extension were developed before Joomla had the tagging feature), but it might make a leaner product in the future.
Personally, I'm in the opinion that one should rely on the core features as much possible.