Unlike the first game, now you can join one of several factions – having special benefits but also disadvantages. Choose carefully because every faction has an enemy, so in case you are friendly with one you become enemy with the other. Some specific armors and upgrades are only accessible in the appropriate factions. Joining a faction also means you will get the best prices when selling and buying stuff with them, which helps you, especially late in the game.
The Loners have Gordon in control, and their enemy are the Bandits in Garbage zone. They get some nice upgrades for low and mid class weapons. Keep in mind the Bandits have the same upgrades as the Loners, it's just a matter of preference here.
Duty are the rivals of Freedom. They are the first to offer upgrades for the shotguns and Russian armors, and the second to upgrade sniper and standard NATO weapons.
My personal advice would be to stick with the Loners up to the midgame.
The swamps are the training level for new players. It gives you time to get used to the interface and the new game options. You might notice how beautiful the training level actually is, full of DX10 effects which you unfuortunately won't see that much later in the game. Maybe 
they are trying to grab you with this first level, keeping your interest – or maybe the effects are just too fancy to pull off when the screen is full of baddies.
In the swamps, you will automatically join the Clear Sky Faction just to see how Faction Wars function. All the guides and transportation are free in the training level, but later on you will have to give your last penny to benefit from these fancy tool.
In the Stalkers base you can steal two AK-47 and a scope, if you manage to climb the roofs and keep above the tech guy. Before you leave the training level, be sure to get the scope from the Lookout Tower, the Viper 5 in the Pump Station, the Chaser 13 shotgun next to the stash in Pump Station and the CS-3 armor – a reward for completing the quests.
Gordon Zone
Starting zone from the first chapter, belongs to the Stalkers. Every time you receive a Stalker task out of this zone, you can grab your reward in the Stalker central to the North, or from Wolf. The nice thing about Gordon is that there are lots of veterans, so if you let them die you might get some good weapons and armors – SPAS 12, Vintar sniper, etc.
Agroprom
This is the home of Duty faction, but there is also a big Stalker camp in the base between the destroyed gas tanks. There is also some shaft with a hermit who offers the best weapons in game. Their prices are insane though. The constant missions for defending the base provide a nice income stream.
You can only upgrade the Vintar snipers in the Duty base.
Garbage
Here you will be in wars with the Bandits constantly. It was impossible to clear their base, but a hot fix came in one of the patches. The only Stalker place you will find is the Flea Market, however all the missions you complete will be rewarded in Gordon.
Yantar
The home of the only neutral and friendly to your faction – the scientists. Here you can buy a SEVA costume. Over the lake you can find two artifacts, one of them is always the Eye – 20 000 rubles in cost. The enemies here consist are zombies and mutants, having a strong shotgun will help you live as the zombies at this point are no longer dying from only a knife hit.
Red Forest
Probably the hardest place ever. The moment you get in you have to chase Strelok, then you get ambushed while having bad armor and rusty weapons. Prepare for lots of actions, anomalies, mutants, artifacts and if you are a friend with Freedom – a battle with twelve heavy armored Stalkers.
A good sniper from the Freedom base will help you get them down easily though.
Two artifacts are waiting for you next to the rocks in the map exit, guarded by a giant Flesh Mutant. I couldn't kill him, so I just grabbed the artifacts and ran away. If you pass these zones you will have enough money and ammunition to continue during the rest of the game, which I'm not going to spoil for you.