In my opinion, getting inside the Colosseum is not worth the wait/crowds. In that area I would rather concentrate on the forum and have a look at the nearby Basilica Dei Santi Cosma e Damiano (5th century), see the Roman Senate building, Capitoline museums, Basilica di Santa Maria in Aracoeli (Rome's titular church). Elsewhere, check out Trastevere for a stroll, a meal and some beautiful churches. You say that you have been to Vatican. What about the Lateran Palace and Basilica di San Giovanni in Laterano? It is hard to recommend without knowing your interests.
And I am definitely in agreement with KLouis - I don't see how one can see everything there is to see in Rome even in a year, let alone a couple of days