Although we've only played with the National Advantages option thrice, each time we agreed that it modified the game too greatly. The primary concern was not that some advantages may be better than others, but that the flow of the game itself was changed for the worse by having these abilities active from the first round of the game (too much colonization, merchant ship imbalance, etc.).
One proposed solution is to treat the national advantage tiles as extra buildings that are available for purchase (exclusive to the respective nation). As such, the tiles would be placed on the board face-up next to the buildings spot and would be available in addition to the standard random draw of buildings. When a player resolves a worker in the building box, the player can choose to build a national advantage "building" instead of one of the randomly drawn buildings, at the appropriate cost for the age. In this way, the game plays out more like the base game.
The primary drawback that I see to this variant is that somewhat fewer buildings will be drawn (as players will sometimes opt to purchase national advantage tiles instead). A further variant could be to remove unpurchased national advantage tiles from the game after the first round or after the first age. Alternatively, an extra random building could be drawn for each round (or each round in the first age). Another option would be to allow one worker to a purchase national advantage tile in addition to a regular building tile (but paying the monetary cost for both).
Thoughts? I plan to try some version of this variant the next time we play AoE.
I find these National Advantage variants to be a significant improvement: http://boardgamegeek.com/filepage/75936/player-boards-for-ea....
The powers are more balanced, and you get some nice player boards for each nation.