subqueries vs. separate queries

Say for argument’s sake I was silly enough to have plugin modify $wp_query before it is run, what would be better, to insert a sub-query or to first separately run the queries I need to run and patch the query via php?

I was assuming the subquery route would perform better, but I also see not all versions of MySQL supports e.g. LIMIT in sub-queries – which, purely rhetorically of course, I might want/need to use.