Swampert is amongst my favourite Pokemon overall, so this is an easy choice for me. Mudkip itself is pretty good too in my book. But I agree that they're all good. Definitely one of the stronger starter sets, if not the best.
Mudkip definitely for me. Swampert is my favorite evolved water starter, and the line is best for me to use for the water-based region. It sure is great in-game with Ice Beam and Quick Claw along with its water type attacks.
Treecko, just because I find Sceptile to be the coolest of the final forms. Grovyle is totally awesome as well. Basically I like the entire line. I like the other lines too, but Combusken and Marshtomp aren't as cool to me as Grovyle.