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Normally I don't worry about natures, but I want to be extra cautious, because Emerald's a lot harder than Sapphire, and Tsunami(Mudkip) still nearly died like 5 times in my Sapphire Nuzlocke. I know there's a best nature for mudkip question, but that's for a normal playthrough(presumably, it's never actually said in what way this Mudkip is used), and I was wondering if it being a nuzlocke would change things. Thanks!

So extra defense would be preferred over sp. defense?
Probably? I don't really know whether an offensive or defensive increase would be better in a nuzlocke, because if you go attack, you can kill faster, and if you go defense, you live longer but take longer to win.
The taking longer bit won't matter as much in a nuzlocke if you're trying to not kill anything.
I mean for like taking out trainer's pokemon, and gyms and e4, not in the case of wild encounters.
Oh, wait, nevermind, I see what you mean.

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It all depends if you want your Swampert to hit harder or take hits better. Through my personal experience, a Relaxed nature (+Def, -Spe) would be better for taking hits better and either Quiet (+SpA, -Spe) or Brave (+Atk, -Spe) if you want an attacking one. Swampert already has low speed, so the slower speed won't make a difference most of the time. For the relaxed nature, most early game Pokemon have physical attacks, including all of Roxanne's Pokemon and all of Brawly's Pokemon. Also, the only attacks on Flannery's Pokemon that hit you for neutral damage at that point would be physical attacks. Brave and Quiet are pretty obvious. Don't go for Adamant unless you're sure that you won't be using Surf or Ice beam. An adamant nature may make it so that you miss out on crucial KOs when using your special attacks.

Overall, I'd say go for Relaxed as it may help in the early game quite a bit and while there are a few special attackers in the late game, you should be able to get a few good encounters to help against them.

Hope I helped.

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I finally got a Relaxed Mudkip! Also, something wierd, I got like 3 or 4 female ones, and all four were Bashful, also, once, when I was nicknaming one, I saw the female sign, but when I checked it's nature, it said it was male, which was weird.
Wait a minute, don't you think Sassy would be better, since most gym leaders and E4 specialize in a special attack typing.(Wattson, Juan, Flannery, Tate and Liza, and Sidney, Drake, Glacia and Wallace)
Wattson and Flannery shouldn't be a problem due to type advantage, since Marshtomp would be immune to electric and resistant to fire. Flannery's none-fire moves are physical. Same with Wattson, however Selfdestruct from Voltorb may be very dangerous regardless. Sidney only has 2 Pokemon in Emerald with Dark type moves, one of them being a Grass type so you wouldn't want Swampert to face it anyways.
True, but what about the others, like the E4, Champ, and 7th and 8th Gym?
Plus the Rival Battles, and battles with Archie and Maxie, who both use Special typings, although I will be resistant to Maxie's fire moves, he also has dark types like Mighteyana, and with Archie, water is neutral damage.
Edited my other comment for Sidney before seeing that you commented, but for the others yeah its true Physical Def won't help it as much but that's what your other Pokemon are for which you should have by late game. You can't rely on your starter to carry the team the whole way especially if they get into an accident.

Also believe it or not Archie has no water moves in emerald no seriously I just checked it now wtf. His Crobat has bite though.
Really, wow that's weird.