The biggest problem with Puerto Rico and Mexico City comes down to geography. Baseball, unlike every other sport, travels overnight 75%+ of the time. Puerto Rico is 1,000 miles from Miami, its closest MLB city and an insane 3,700 miles to the farthest MLB city, Seattle. Mexico City is less obnoxious for every trip but it still has a lot of teams traveling considerably farther than normal overnight. Mexico City is 2,200 miles from Boston and 2,300 miles from Seattle.
Mexico City is perhaps feasible but I just don't see how San Juan is a real candidate for MLB expansion (ignoring the difficult economics of both regions in comparison to mainland US and Canadian cities).