They're both good civics. It depends!
As everyone has said already, Mercantilism has nice synergies with Representation, the Pyramids, the Parthenon, and Caste System. And if you're Philisophical or running Pacifism, the double GPPs make it even nicer.
On the other hand, those extra trade routes do add up. On a standard map, by the middle ages the trade routes will be running 4 to 6 commerce each in your core cities. To keep things simple, let's say you're running 50/50 gold/science. That's 2 or 3 commerce for each, multiplied by probably 50% for buildings (market + grocer, or library + university... will be less in some cities, but much more in the capital with an Academy or University of Oxford.)
So, 3 to 5 each of gold and beakers vs. a free specialist. If you're not running Representation, it's no contest -- trade routes are better; the extra route is like having a merchant /and/ a scientist. If you are running Representation, it's competitive.
There are other complications (how much are those GPP worth?) but that's a rough sketch.
As other people have pointed out, Mercantilism becomes more attractive when your empire is bigger. On the other hand, Free Trade gets more attractive in the late game, when AI cities are big (because trading with bigger cities gives better trade routes).
Waldo