I've spent some time in both Bogota and Medellin and gave short talks in biggest startup hubs of both cities (HubBog in Bogota and Atomhouse in Medellin). There seems to be an energetic startup vibe in both cities, but the biggest difference I noted was the level of how international it felt. In Medellin there were plenty of foreigners and locals had no trouble conversing in English, while in Bogota most of the folks at a startup event with an English speaking guest speaker could not pull off their 2 minute pitches in English. I found that the most surprising difference.
Surely my sample is not big enough for serious conclusions, but hopefully it provides an additional dimension to keep in mind when making your choice of the city to go chasing opportunities in.