Yep, Japan has a pretty big advantage with so much food on the map. However, they are not really the most powerful civ. That would be the Zulus. I would put them at the end of the first tier:
For me , its 1,2 ,3, 4>> Zulus, Americans, Chinese, Japanese
The it drops down to Egyptians, English, Spanish, Germans, India
The Zulus have all these amazing bonuses. 2 movement warriors is just incredible in the early game. Then they get Rapid city growth, which basically offsets Japan's advantage in food. After that, they get +50% gold production. These advantages are just so powerful and flexible that they combine to make the Zulus second to none.
The Americans start with a Great Person, which is pretty nice, since you can explore a bit for the first few turns and then either settle or cash in the GP before anyone, even the French or English, even get a GP. Then the Americans get half cost unit rush buys. This is by far the best ability any civ gets. It is not even close. Finally, They get the triple production factories, which in my opinion, is the best Modern Era civ ability.
The Chinese with their +1 city size from the start of the game have probably the second best advantage in the game. They also get two very helpful techs (writing, literacy) by the time they enter the medieval period. Writing, especially helps because it is on the path to Code of Laws. Since Chinese cities are born size 3 in the ancient period, China gains the most by teching to Code, entering republic and cranking out settlers before the price to rush buy them goes up.
Then Japan, as discussed. Oh, and the +1 Samurai Knight Attack is kind of nice, too.
The thing which sets these four civs apart is the way that their abilities are helpful no matter what kind of victory you want and no matter what kind of map you are on. The second tier is characterized by a lot of abilities which only help certain kinds of victories or on certain maps. If your map has a bunch of whales, then Spain rocks. Ditto for the English and Dye. The Egyptians are the most up and down of all the civs. If they get Colossus as their wonder and are near a bunch of deserts, look out! If not, well, they are just ok.