Are the legendary dog/cats and birds in Colosseum?

[Rekkuza]

If they are, what level are they at when you encounter them?

[Kari and Mewtwo]

No birds. Only the beasts. All 3 of them are at lvl 40.

[Dark_Alakazam]

1 bird Ho-oh. Purify all 48 shadow pokemon and then beat 100 battles on mt battle in colloseum mode. I did it, not so hard at all.

[Rekkuza]

If you fight the trainers with Entei Suicune and Raikou but accidently knock them out, will you be able to catch them later? And when?

[Number1ChanseyFan]

Yeah, you will get another chance to catch Sudowoodo, Raikou, Entei, and Suicune in the Realgam Tower, when you have to defeat Miror B., Dakim, Venus, and Ein to get the ID Badges. However, it would be a good idea to just save your game before you face the trainers with these Pokémon, so you can simply restart your game just in case you fail to snag their Pokémon. :)

[Don't Run With Scizors]

You can fail to snag their Pokémon as many times as you want. All the trainers in the game with Shadow Pokémon will show up somewhere else in the game no matter how many times you beat them (with the exception of your double with the Togetic at the end of the game), and they will keep their Shadow Pokémon with them until you snag it.

In the case of the Cipher Admins, they also show up in the Deep Colosseum after you've beaten Evice, and they will stay there forever.

[DarkestLight]

Oh really? I haven't had time to consistently play this game and so I just got up to the last guy in Realgem the first time and kicked the bucket...so much money lost. Now I'm upset I wasted all that work for that stinking Metagross >< when I could have killed it and kept all those pokespheres.

[Moonlight Espeon]

The three dogs/cats are with the Cipher Admins, the only Cipher Admin without a legendary is Miror B. who has a Sudowoodo instead.
Cipher Admin Dakim- Entei, Lv. 40, final battle at Mt. Battle when Cipher invades it
Cipher Admin Venus- Suicune, Lv. 40, battled at The Under when in her studio
Cipher Admin Ein- Raikou, Lv. 40, final battle at the Shadow Pokemon Lab

[TheParadox]

Are there any Decisions that need to be made (e.g The fossils in RBY) and how far in is the Earthquake TM

[Number1ChanseyFan]

Are there any Decisions that need to be made (e.g The fossils in RBY) and how far in is the Earthquake TM

TM 26 (Earthquake) is found in the Shadow Pokémon Labratory, which is later in the game.

As far as decisions that have to be made, there are no real major decisions where you have to choose between certain things. Early in the game, in Phenac City, you will have to choose which of the 3 G/S/C starter Pokémon that you want to attempt to snag, Bayleef, Quilava, or Croconaw. You will still be able to get the two Pokémon that you don't snag, but you won't get the chance to get them until the end of the game. Actually, you can't get them until "after" the end of the game, since you have to beat the game (a.k.a. defeat Evice at the top of Realgam Tower) before you can catch the other two G/S/C starter Pokémon.