My opinion is that we'd be better off "rolling our own" as I did with the old perl software, using dbm files and updating the search engine nightly.
The nice thing about using MySQL as the search engine is that we get it "for free". The data is in the database anyway, so why not just let MySQL handle it?
But the downside is that we have to more or less accept all the quirks (or lack of quirks!) that come with the MySQL behavior.
If we roll our own, then we get to preprocess the text in any way we like, plus we get to *score* the results in any way we like. We can do neat things like taking care of the wiki syntax optimally. We can do things (in theory) like scoring an article slightly higher as a search result if lots of other articles link to it. We can give higher points to italicized words, maybe.
We can choose to handle singulars and plurals in any way we prefer.
All of these things will be a more or less empirical matter, but my own experience suggests that some tiny clever tricks can massively improve the relevance to the end user.
--Jimbo