Marowak and Aerodactyl are already viable Pokemon as it is, but it seems illogical to me that they didn't get Head Smash.
You can breed Ironhead into Marowak, i think Aerodactyl too.
Kingdra:
Flamethrower (Breed)
More Physical (Iron Tail?)
NidoKing/Queen:
Poison Jab (Lv)
Roar (Lv)
Irontail (Lv)
Sceptile:
Petal Dance (Lv)
Milotic:
Return (Lv)
Dragonite:
Draco Meteor (Lv [I say at lvl90])
Meganium:
Energy Ball (Lv)
Flareon:
Fire Fang (Lv)
Thunder Fang (Heart Scale) <-- to make up for not giving it a physical fire move in the beginning
Glaceon:
Ice Beam (In place of Ice Fang)
Kabutops
Leaf Blade: (Breed somehow)
Guillotine (Lv)
Tyranitar:
Splash (Replace all moves)
Aggron:
Meteor Mash (Lv)
Gyro Ball (Breed)
thats all i'll do for now..
Raikou needs a movepool other then Thunderbolt/Calm Mind/HP Grass/Reflect or something like that.