I would think that one tradeoff is a metaphone analyzer implies that one can only
search w/ metaphones and can't do a more direct, exact spelling, search, while
the metaphone query can be used on any index (at the cost of the dreaded term traversal).
An analyzer does not have to replace terms, it can also place metaphone encodings in the same position, using setPositionIncrement(0). There are some fiddly issues that occur when position increment zero is used, however - for example it is not possible to use that same analyzer with QueryParser and have phrase queries work properly (but there is at least one nice workaround).
So, exact spellings can be made to still work.
Erik
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