Lucario! (you knew it would me who replies first )

the Mouse Pokémon. It can generate electric attacks from the electric pouches located in both of its cheeks.

Errh... is it Mawile?

This marine Pokémon has an impressive build that lets it freely fly over raging seas without trouble.

Voltorb! (or Electrode...same thing)

It slumbers at the bottom of a deep trench. If it flaps its wings, it is said to cause a 40-day storm.

That's easy. Lugia!

Also, it's not Manaphy, it's Dragonite.

It was created by a scientist after years of horrific gene splicing and DNA engineering experiments.

I figured Aaron's was Kyogre, lord of the sea.

I know that one Alex:
Mewtwo!

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I am thinking of a very negative pokemon.

Is it Minun?

Also, Kyogre doesn't have wings...

Commonly found near mountain trails, etc. If you step on one by accident, it gets angry.

I believe that's Geodude.

Even though it has no eyes, it can sense obstacles using ultrasonic waves it emits from it mouth.

Persian.

It makes a thin entrance in it's nest to get through. Only it can fit through this hole.

you gave a hard 1 Flint.
The pokemon is the spider one, Ariados or something.

This legendary bird Pokémon is said to appear only when a thundercloud parts into two halves.

No, the one Flint described has got to be Arbok!
And yours is Zapdos, obviously.

This Pokemon leaves behind it a rainbow when it flies.

...Pachirisu?

This Pokémon wanders across time. Grass and trees flourish in the forests in which it has appeared.

Shu... Sha... That bush one... the one that can turn into a reindeer...

Shaymin? Something like that...

It is able to take in large amounts of air and dive to incredible depths with just one massive breath.

Hippowdon.

Its first evolutionary form is very, very, very weak. Once it evolves, it becomes VERY powerful.
Extra Hint: (Water type, was owned by a Team Rocket member at one point)

Karpador (ger) Magikarp (eng) ?

Which pokemon got the most evolutions, and what name do the evolutions have?

Eevee has got the highest number of evolutions (though it can evolve only in one of these):
I° gen.

Vaporeon
Flareon
Jolteon

II° gen.

Umbreon
Espeon

IV° gen.

Glaceon
Leafeon

(I love EEevolutions )

my pokemon is very active in the night and is usually followed by a lot of his pre-evolutions

I know this one! That orange otter Pokemon! "Buisel" I think

While seeking iron for food, it digs tunnels by breaking through bedrock with its steel horns.

tentacool!

Photosynthesis occurs across its body under the sun. The shell on its back is actually hardened soil.

Flint, mine was Honchcrow ^^ not Gliscor

Your's is Chinchou or Lanturn I think

It has the power to predict the future. Its power peaks when it is protecting its Trainer.

No, wrong again, is Gardevoir

Sableye

Very smart and very vengeful. Grabbing one of its many tails could result in a 1000-year curse.

Ninetails.

(NO, IT'S A JIGGLYPUFF SEEN FROM ABOVE. *shot*)

The only Artificial Pokemon (that is, created by humans), it is the only Pokemon that is a copy of another.

Well, should be Mewtwo, but Porygon/2/Z are artificial too if I remember right :\

When the heavy rainfall season ends, it is drawn out by warm sunlight to dance in the open.

Sentret

When it sleeps it turns to stone.

It's Graveller!

Has steel-like hide that makes it's powerful tackles even more dangerous. It's horn is hard enough to pierce a diamond.

Rhydon!

It has the ability to foretell natural disasters. Its life span is over a hundred years.

(That last one was actually NidoKing. >>)

It's ABSOL!

During the daytime, this Pokemon plants itself in the ground. It is rumored to change the shape of it's feet to become similar to the roots of trees.

Sudowoodo?
This pokemon, with great psychic powers, was created as a result of a genetic experiment.