It seems quite a few of the legendaries are based on at least a few gods from different cultures.
As for Greek gods..
Zeus- Thundurus, he just seems like it :o. Zapdos is also a possibility, but not as much.
Hephaestus- Arcanine. Being the god of fire and all, and I have always thought Hephaestus would have that grizzly look.
Aphrodite- Jynx. Yeah yeah, quite ironic, the goddess of love and beauty looking.. Like that? XD. But if you think about it, Jynx's moves sometimes seem to be centered around capturing the opposite genders "heart" and making it fall in love. Could also be Eros, the god of love (Or Cupid.. Take it as you will, they are virtually the same >_>)
Apollo- Moltres would be possible, since it flys (going with the whole "Chariot of the Sun" thing) and it is a fire bird..
Gaea- Groudon. If you cant see the connection.. Well Groudon is a Ground type, and it is said he shaped the land.. I think o.o. Same with Gaea, only SHE is the land...
Poseidon- Kyogre would be an popular choice, for obvious reasons.
Ouranos- Arceus. Yeah yeah, you can say Arceus is like the "Top dog" but it does state he might have possibly created the universe, and the pokemon world at least. Ouranos was thought to be the creator (At least, as far as I know, though I may be wrong) of our world
Hera- Truthfully, no clue. It could be Articuno, but there is nothing that I know of that could tie these two together..
Hades- A plausible choice could be Giratina.. >_>
Hermes- Pidgeot perhaps, going on the fact thats it pretty darn fast and would be a good messenger bird eh?
Also, for the person who stated something about laymans grasp blah blah, does anyone really completely understand Greek mythology? I doubt the Greeks themselves fully understand every aspect of it. Oh well, if I got your meaning wrong.. Bite me~~