How about being bombarded with respawning enemies? Did you enjoy that? Going through the same checkpoints that you have already cleared 100 times previously fucking sucked... period. The Malaria? I found it to be nothing but an annoyance that made me go out of my way to get medicine and soon became about as repetitive as respawning enemies. As for the atmosphere, yeah I loved it. I thought it was a fun game on the whole outside of said issues that ruined the immersion.
In Far Cry 3 there is more to do in the world, without being knocked out of that 'I want to explore' mood these games are made for. Instead of respawning enemies in jeeps flying over cliffs and landing on your head every few minutes, you are encouraged to go out and find upgrades, ingredients and take over bases that become yours. Places you can customize gear, craft items, fast travel and take on new side quests. The world is crafted to be enjoyed more, while giving you a sense of taking it over.
One other note on the Malaria being cut. Here you actually get to mix ingredients and take hallucinogens that not only provide some gorgeous visual effects and even induce a sense of insanity at times, but gives you benefits as well. Such as being able to breathe longer in the beautiful underwater environments, while looking for secrets and tangling with the occasional a shark or two. Much better than, "oh god, time to go through 5 respawned checkpoints or take a bus to go to the doctor before I can continue the game." The tension they wanted to create only added tedium for many of us. It really sapped the fun and sense of immersion out of an otherwise gorgeous world.