They are good for different reasons. Troubadour is only like 320 capacity, so it's really intimate, but its not nearly as nice as the El Rey, which is bigger and sounds better I think. I like both though.
I like both, The Troub is tiny and you could just stand by the bar and not feel so far away watching. I really like the El Rey though since more shows have been popping up there in the last couple years and its nice and sounds good.