My favorite antagonist is Vaas Montenegro from Far Cry 3. Vaas is like the head of all corrupt forces o the island. Vaas will stop at nothing to bring down the Rakyat tribe to get what he wants. Even going as far as killing Jason Brody once and for all.
Vaas is a character that you love, but also hate at the same time. He can be cold-hearted and cruel sometimes, but yet protective over his sister Citra at the same time. It gives you a little to see in him but not enough to actually want him to survive.
It would be really awesome to see through his point of view and hear what he thinks. Or even to hear his thought process.
A backstory is definitely a must to add to the list of ways to improve Far Cry 3. Other than that I don't think any other improvements would be needed.