For my Emerald nuzlocke, I decided upon using Treecko instead of Mudkip due to me using it all the time. It managed to do well against a couple gym leaders (Roxanne, Wattson, Juan), but it had to take a backseat for most of the E4, it did assist with Sidney and Phoebe a bit, but it couldn't do much against Drake (as I taught a different Pokemon the Dragon Claw TM), Glacia, and even Wallace as half his team had Ice/Poison coverage. From what I heard from other people, Blaziken isn't too good, so I assume that the gen 3 starter ranking is something like Swampert > Sceptile > Blaziken.
I ended up getting many ideal Pokemon as well such as Azumarill, Breloom, and Manectric, so that probably ended up making the run much more easier. Overall, I think Swampert is still the best in Hoenn regardless of which game you're playing.