PokéBase - Pokémon Q&A
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Garchomp is by far better at stats than flygon

http://pokemondb.net/pokedex/garchomp
http://pokemondb.net/pokedex/flygon

Both have similar movepool so id choose Garchomp because its better and can learn Dragon Rush

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Atcually dragon rush sucks. And Flygon can learn better moves
they both learn dragon rush now in gen 6.  Source: pokemondb.net/pokedex