That depends on what you mean. Which do I like better look-wise, or which is stronger. If you asked me to vote based on looks I would choose Pikachu. Also, since the topic is Pikachu Vs. Mudkip and not Pikachu Vs. Mudkip and all its evolves, then I would still choose Pikachu.
Also, can anyone tell me where that Mudkip craze came from? It's confusing the heck out of me.