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I liked Ruby a lot because you got to battle Team Magma :p But I really loved Emerald because you were able to battle both teams and it had new features.
I prefer Emerald on almost all terms except that it's missing some of my favorite pokemon. The biggest offender is Masquerain, who is in my top 5 Bug pokemon conceptually. Other than that, I generally take Emerald and any of the 3rd in the set of any of the generations. Yellow, Crystal, Platinum, you name it!