I can give my opinion on the strongest non legendary pokemon but that's all it'd be as each pokemon has a certain weakness (except magikarp of course) and so you can't truly say this is stronger than that pokemon.
http://www.serebii.net/pokedex-dp/stat/all.shtml
Above is a list of all the pokemon listed in order of their total base stats and according to that list, the non-legendary with the highest stats is slaking.
PIKACHUUUUU
lucario
Reshiram. But if you make any other Pokemon stronger than it by level, yes, then it will be that Pokemon. But if you look to it by the side of legends and legendary power, it is Reshiram.
Probably either Spiritomb or Garchomp
the strongest water Pokemon is Palkia
ummm, this is a hard question and it comes down to Politoed, Gyrados or Palkia, and I would HAve to go with Palkia because he's a legendary and he can learn a lot of moves, of course, Gyrados is a unpredictable Pokemon because he can learn fire moves, dragona and water moves
well the strongest Pokemon you can catch is raqazza a legendary dragon Pokemon
The strongest dragon type in pokemon Emerald, Sapphire and Ruby, is the legendary pokemon Rayquaza. In terms of non-legendary pokemon, both salamance and flygon are strong dragon types.
I think , all of the legendary pokemons.
Rayquayza
shymin
Moltas: the fire legendary bird Pokemon the second strongest bird Pokemon