The ideal of ES when they designed the game was, of course, to create a playable, yet somewhat historically accurate game.
Basically, my idea for balancing greeks might be something along the lines of Neil's, except for the fact that I would generally give Hoppers a +1 Piercing Armour (they do have shields, after all - even without any Shield techs). Combined with the Bronze Shield, this would make Greek Hoppers stand up better to archers. A problem will, of course, arise with Mace (+4 piercing armour in Bronze?!) --- generally, Archers would still be the bane of Academy units, they just wouldn't own them quite as much.
Another alternative idea for a kind of economic bonus for the Greeks would be to give them cheaper techs - say 25% or 30% off for all techs. This would be in line with the 'Greeks invented everything' sentiment some people have about the world of antiquity.
Yet another option might be to give Greeks both Fire Galleys and Cat Triremes in Iron, or change the Cat Triremes for Fire Galleys. Of course, this would accomplish nothing but making Greeks stronger/different in Iron ... and having all three ship types would probably be overpowering but still ... 30% faster Fire Galleys would be fun. Generally, I still find naval warfare to be about the most boring kind there is. If there was a wider selection of warships earlier, it might have been fun. But as it is, it is kind of dull.
As for Carth, I'd rather give them some kind of trading bonus ala Palmy than a fishing ship bonus --- it would be better suited to their history. As an option for the fishing ship bonus, I might suggest something along the lines of Farmers that gather food faster, say at .45 or .50 --- I know some people's Villagers aren't born to farm, but some of mine are. This would also be a very good bonus on Hill Country, I believe, whereas the trading bonus would not.
Another thing might be to make both Greeks and Carthaginians eligible for full Priests.
All the ideas I've tossed around above are at based at least somewhat on history, more than game balance, even though that's what the intention is.