I get the appeal of a safe Water pick while learning the routes, and it makes sense that Mudkip carried a lot of fights for you. Switching to Treecko on a replay is a nice way to change the pacing, though its early moves can feel limited until it gets going. Torchic does seem like the challenge pick, especially against the first gym. I haven't played Emerald myself, but hearing how the choice reshapes the early game makes me curious which one feels most rewarding long-term.