Because anti-free traders such as the Canadian socialists Nicmarlo mentioned are able put immense pressure on these trade agreements. Trade is just like the tax system in that, when they're done right, simplicity and transparency go hand in hand in both... Free trade depends on competition, not harmonization, and its only the harmonization aspects of NAFTA that one should worry about from the standpoint of sovereignty. Look at the history of anti-trade movements. Guys like Nader, the Know-Nothings, Hugo Chavez and the rest are able to arouse enormous resentment and passion.
The reason trade agreements are so tough to put through in a form that isn't overly complex is that every special interest wants some exemption that that favors themselves: car makers want tariffs on cars but not on steel. Combined with the lack of support for free trade from anti free market "right" wing types, governments sometimes try to appeal to the Left--- "hey, look, we're really just trying to keep those nasty corporations from benefitting from slave wages in Mexico" by introducing harmonization elements in trade agreements.
The tax cuts President Bush pushed through aren't perfect, either. But the perfect can't be the enemy of the good. The answer to a complicated tax cut bill is not to say screw it and then raise taxes. The answer to overly complex free tarde agreements is not to raise tariffs and duties or to otherwise restrict the freedom to buy and sell, but to support its simplification.