If we're still trying for a 3rd-gen pokemon, I've got an idea to throw out. It's a bit of a longshot, but Mudkip
might work. Mudkip has alot of love/hate among the fans nowadays due to it's meme status, and could be given a pretty unique moveset for those worried about it being a squirtle-clone.
-Ah whatever, I'm bored, so I'll come up with a moveset for Mudkip "just because."
B: Mud-Slap
Mid-to-short ranged semi-rapid projectile attack. Tapping B will have Mudkip kick-up a spray of low-damage streams of mud forward. Like the firebreath moves, it gradually becomes less effective, but instead of loosing range into nothingness, it sprays less mud-streams, to a minimum of one stream.
Side B: Water Pulse
Essentally, Mewtwo's Confusion attack with longer-and-wider range, and less damage. It would have to be a bit slower so it couldn't be spammed as rapidly as Confusion could.
Up B: Mud Sport
A clump of mud appears below Mudkip, and it uses it as footing to jump off of it in the tilted direction. The mud clump bursts a bit like a firework, flinging mud all about and pushing away anyone(friend or foe) that is too close to the burst. When used on the ground, the burst would be a bit wider.
Down B: Bide
It would be a counter-type move. A mix of Wario Waft and Mr.G&W's cup-thinger(I forget what it's called.), it would have to withstand enough damage, which gets save up between uses, until Mudkip begins to flash. While flashing, the next use of Bide would unleash a high knockback attack of some kind.
Final Smash: Whirlpool
Whirlpool would make for a unique Final Smash. Take what they did
in the anime, and make it bigger and more dramatic. Throw in a bit of mud in that spinning vortex of watery death for good characteristic measure.