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I just restarted Sapphire and am choosing a Pokemon. I have chose Torchic before in the past, and it served me well, but I have also seen how powerful Mudkip can be. I have done some research and they are both duel type, pretty good Pokemon. I really can't decide. Is there a way to get either of them later on? Which one is better for early game or late game? Thank you!

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You absolutely want Mudkip, it's no contest. It's super effective against Roxanne and has a neutral matchup to Brawly. It's a Marshtomp by Wattson, meaning it has STAB super effective moves and an immunity. It stomps Flannery into the ground, you can give it Protect or Dig to stall out Norman's Slaking, it has a decent matchup against Winona, Tate & Liza's Pokemon are weak to Water, Swampert is neutral to Wallace, and it performs very well against Steven. Additionally, Blaziken is weak to the plethora of Water types in the game.

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Getting a Mudkip to learn protect before Norman is very difficult. Dig is a much easier way to defeat him.
Edited, thanks.
Are there a lot of fire types? You mentioned there was a "plethora" of water types in the game, which makes me think that I would have a lot of options for other water pokemon if I didn't choose mudkip.
You have a ton of other options, but none are as good. There's Lanturn, Gorebyss/Huntail, Tentacruel, Walrein, Pelipper... the list goes on. Tentacruel is a good HM slave, but Swampert is far and away the best Water type offensively. The other accessible Fire type is Camerupt, which can be caught as a Numel, but you really don't need a Fire type in Hoenn.
well it seems like mudkip is more powerful, but there arent many fire types other than torchic.........
Did you read what he said? There’s a plethora of water types. That means if you really want a fire type, you’ll have to deal with a plethora of Water types. Also, I play through Hoenn with Swampert, and every single play through I do, Swampert ends up overleveled, even when I don’t try to train it. It’s just really great in these games. The extra ground typing sets it apart from other water types, as instead of getting beaten up by Wattson and other electric trainers, it destroys them. Also, as mentioned, it is amazing on offense, and it also can serve as an HM Slave (of course, you’d give it the strong HMs, like Surf, Waterfall, Dive, Strength, etc. since it’s strong). There are few to no instances where you should use a Fire type that Swampert couldn’t do as well anyways.
ok ok choosing mudkip now
@sumwum How do you beat Norman's Slaking with Dig?
@blaziken, it has it's ability that only lets it attack very other turn. so if you can align dig with the ability, you can be underground every turn he can attack