Far Cry 2 was well-liked, but held back by a few common complaints. Ubisoft is hoping to correct that in Far Cry 3, and has talked about some of the lessons it learned from feedback to their previous game.
For example, malaria is something you likely won't have to worry about in the sequel. "I think most people found it frustrating," lead designer Jamie Keen said. "Though some found it interesting because it was the world around them. There are points where we make you do something to pull them along, but we want to make sure we're not contriving situations too much."
Keen also pointed out that you could "get a bit lost" in the vast open world of Far Cry 2. "It's important that it has that sense of exploration, but it needs to be getting towards something," Keen told IGN. "You never want to feel like you're not getting anything back from the world or that you have to wait a while until you get to the next place." He cites the diamonds from FC2 as an example of a game mechanic that had a reward incentive, and points to animals to hunt and money to find as the Far Cry 3 equivalent.
Meanwhile, producer Dan Hay said that the game will let the player have a big impact on the world, but is playing that detail close to the vest. "There are places on the island where - and I can't go too deep into this - once you go in and start to affect that place... Vaas's personality starts to diminish. You're not going to see guys walking around with AK-47s. You'll start to have an appreciable effect on the environment." He says the team has given a name to this system, but he can't say it yet.
Ubisoft has certainly had some time to let the dust settle and look at Far Cry 2 with clear eyes. The game was released back in 2008, so we should see some marked improvement when Far Cry 3 hits in September.