As can be surmised by my avatar, I'm a huge fan of Rain.
He was my absolute favorite character in MKT,
even without using the infinite kick trick.
I loved how all three of his moves were "free hit" moves,
and could be chained together fairly easily.

I was glad to see him again in Armageddon,
but rather disappointed by how he turned out-
He felt like a watered-down (ha ha) Liu Kang clone or something.

I would love for him to be in MK9, in the spirit of his MKT moveset.
I like the story they came up with for him, and I think he can be easily worked into the main story-
he and Kitana could be together initially, when Kitana is still working for Kahn.
Part of her story could involve the heartbreak of leaving her former love because he still sided with her mortal enemy.

Anyway, I know this is a bit long, but I really hope my favorite character makes the cut, and with his moves from MKT intact.
He can keep the teleport and Liu Kang kick from MK:A, but *please* have all three of his moves from Trilogy...
Frozen Rain Orb/Mind Control Orb is my favorite move in the whole series!
EDIT: Here is the updated move list I came up with for my pal Rain-
Lightning Strike- His only surviving move, and yet Nightwolf still steals his thunder(bolt)! This would be just as it was in MKT. Super version calls a larger bolt which hits them anywhere on the screen if they don't block.
Tempest Kick- The reincarnation of super roundhouse, identical except some extra wind FX. Super version also does an electric shock and can hit through a block.
Waterspout- Functionally identical to Mind Control Orb from MKT, but involves a thrown ball of water which erupts into a vortex of water upon contact, and can be controlled with the D-pad. Super version flies faster and controls them twice as long.
Stormchaser- His Liu Kang kick from MK:A. "Windy Feet" just sounds really dumb, IMO! Super version knocks them across to the other side like Tempest Kick.
Evaporate- His MK:A teleport. Super version- he reappears with a Lightning Strike, appearing under the opponent, and bouncing them up if they don't block.
Squall Counter- He reaches toward his opponent. If this intercepts an attack, he grabs them and then blasts them with a giant jet of water from his fist, knocking them far back. Super version forms a large bubble around Rain, extending the range he can counter from, and reflecting any projectiles that hit the bubble.
Throw- he forces his hand over their mouths, pouring water into their lungs.
He then jump-kicks them to the left or right as they cough the water out (looks like they're vomiting water).
X-ray: Typhoon Trauma- Rain grabs his opponent like in Squall Counter, but if he connects, he holds them in place while he summons a Lightning Strike. He bounces them up, then connects with a Tempest Kick, shattering his foe's chest and ribs and knocking them off the screen. As they fly in from behind him, Rain turns and does a potent uppercut, knocking them up and off the screen. In an homage to his other MKT fatality, they fall back upside down, and break their neck and back on the ground.
Finishers: Watery Grave- you had a really awesome idea, NoobSaibot5: Rain surrounds his foe with a big bubble of water, then closes his fist and causes them to explode from the water pressure, turning the entire bubble red. He then releases the bubble, which splashes down and reveals their mutilated corpse.
Dessicate and Obliterate- Rain draws every drop of water from his opponent's body, leaving them a dried husk. Before the husk can fall over, Rain releases the gathered water back at his foe in an explosive blast, disintegrating the dried remains.
Hurricane Kick (heh heh)- Rain Tempest Kicks his foe so hard their torso separates from their legs. He catches the torso as it flies in from behind him, then lifts it up and summons bolts until the torso is nothing but charred remains.
"Klassic" Fatality- his original death-by-lightning fatality, updated so he blasts a couple of limbs off before destroying them utterly.
Hara Kiri: Storm Safety- (another nod to one of your ideas, Noob) Rain sprays his legs and feet with water from his hands until a puddle forms at his feet. He then takes out a sword/dagger, and hoists it high in the air. Lightning strikes, and his head explodes.
Friendship: Rain Dance- in return for Nightwolf's theft of his Lightning Strike, Rain dons a cheesy feathered headdress and does a Native American raindance, summoning a downpour followed by a rainbow in the sky.
Intro- water wells up from the ground, forming a watery human figure. Lightning strikes the water man, splashing water away and revealing Rain. Then he says, quietly and confidently, "You have drawn your last breath!" (a reference to his ability to drown his foe).
Winpose- he flings his projectile into the sky, which explodes into rain clouds and begins to rain down on the entire arena while he stands with arms crossed in a detached and arrogant manner with a bubble surrounding him, keeping him dry.