You're right, it is like GTA in that regard. What threw me was the expansiveness of the world - it just beckons to be explored, but unlike Skyrim which encourages exploration, FC3 discourages it with the save system.
It also discourages replays. I played some sections of Far Cry 1 and Crysis over and over again, trying different approaches and tactics, just for fun. You can't do that in Far Cry 3.
I just cleared the Medusa, and my wish to do it undetected was stymied by the very last enemy. In other games, I could reload a save and do it again, but not in FC3 - my previous save was from the day before (I tried to save it earlier, but couldn't because the mission had already started), and the autosave was already written over.
This article kind of sums up my view of it.