Yes, I've implemented anagram querying as you indicated, by sorting the letters, but the query I have in mind would allow some wildcards as well. An example comes up in scrabble with the blanks, and we've been asked to implement this for some dictionary sites. I was wondering if that could be implemented in Lucene as an FST: I suspect it could, but my brain went numb trying to come up with a regex as a way to get there, and then I ended up building using a direct hand-coded term scanning approach.
Re: the question of mapping queries, I may very well be missing something here. Maybe I've misunderstood your plan: isn't it that Phrase-type queries go through the phrase-analyzer, TermQuery goes through the regular (query) analyzer, and MultiTermQueries go through the wildcard-analyzer?
It just seemed to me that there might be new Queries written in the future that might not easily be categorized into one of those classes, or that it might not be obvious how to indicate which class is thr right one, and it could be handy to have a way to associate them with an analysis chain in the way you've described. Although it seems that my one example probably falls into the MTQ category and I guess would just pick up the wildcard analysis chain, which is probably the right thing.