The nature of the foe: Colombia's decades-long conflict with the FARC rebel group and with powerful drug cartels is motivated, at least on the rebel side, by a Marxist ideology aimed at overthrowing the state. In Mexico, the drug war is motivated by the cartels' basic goal of moving narcotics into the U.S. without government interference, and collecting profits.
Territory: At the peak of its power, the FARC controlled a "Switzerland-size chunk" of Colombia's territory, with identifiable borders, plus other land. In contrast, Mexican drug gangs' sway over certain regions of Mexico remains fluid, and there is "no zone the Mexican army cannot reach when it wants."
Targets and tactics: Terrorist-style attacks have occurred in Mexico's drug war (a remote-controlled car bomb in Ciudad Juarez, a grenade attack on civilians in Michoacan) but they have not occurred with the frequency and scope as such tactics in Colombia. The Mexico drug war is mostly a conflict between feuding cartel groups.
State weakness: This is where the line is fuzziest. Colombia had a weakened army when the FARC began attacking the state, but a relatively strong civil society that eventually rose up and demanded solutions. Mexico sent 50,000 troops head-on to combat its drug gangs, but it has so far fallen short in pursuing desperately needed reforms in the justice system, for example, and in money laundering.
Taking that a step further, even if you accept that their similarities are important, I don't really know what the implications are. A Plan Mexico for Colombia is where a lot of proponents of the analogy go, but it is there in particular that the comparison falls apart, because, even after a decade of Plan Colombia, the nation remains the world's premier cocaine exporter, it remains far more violent than Mexico (though safer than 10 years ago), and Plan Colombia was successful only insofar as it helped beat back the Farc, a group that has no corollary in Mexico.
Discarding that, what does the comparison tell us? OK, Mexico could use a more trustworthy judiciary and police force, but who couldn't? It's kind of like telling us that Delhomme needs to throw less interceptions because Peyton Manning does; we don't need Manning's example to know that turnovers are bad.