For the different combat modes, there are different set of weapons: In armored mode, the player can use mostly the same weapons as he did in the Bioshock 2: a drill, a rivet gun, a hack tool, a double-barreled shotgun, a camera, a spear gun and a launcher. The machine gun is swapped to the ion laser.
In unarmored mode, the weapons are similar to the ones in the Bioshock 1: a wrench, a pistol, a machine gun, a shotgun, a grenade launcer and a crossbow. The hack tool and the camera shared with the armored mode.
In the underwater mode, the player use the same weapons as he did in the armored mode, but only some of them. The drill, the rivet gun, the camera, the spear gun and the launcher ( only a specific shockwave gremade) are available.
The system of weapon upgrades are reconstructed. There are two type of upgrades: the usual ones for the two set of weapons, and the so-called ammo upgrades for the Big Daddy weapons. These upgades allow the player to use specific ammos like trap rivets, nails, gamma laser or shockwawe grenades.
The plasmid development system changed significantly: instead buying the higher level of plasmids, the player can improve his basic plazmids with augmentation chemicals. Each plasmid has three augmentation slots, and the player can place augm. chemicals in them. The same chemical has different effect to the plasmids. For example, the Wall augmentation with Incinerate! creates a wall of fire in front of the protagonist. With Telekinesis, the player capable to produce the effects of the Sonic Boom plasmid.
The biggest change in the gameplay is the armoury of the Splicers. Instead of using the same weapons and Plasmids again and again, each Splicer has a loadout: max. two weapons (both one can have an upgrade and a spec. ammo type), two plasmids (+one augmentation for each one), a special slot for grenades, and three slot of tonics. It's guarantee that each enemy will be a new challenge.
The usual types of enemies out of the picture, so the research system must be changed too. Now each research prize has an own research track. The prizes can be Gene Tonics, weapon upgrades or augmentation.The other big difference that the player won't get the obtained prize directly fom the research camera. The player get just a recipe, what he must assemble at an U-Invent station on his own.
The U-invent stations has great importance in the Bioshock 3. Here the player can not just making new ammos, but assembling the research prizes, upgrading his Security Bots or even disassembling spare ammo into new components.
Intsead of being independently placed, now all security devices are under the control of the local Security Station (used to called Bot Shutdown Panel). After hacking the Station, the player can control the security forces of Rapture: maintenance his own bots, trigger alarm on the other end of the level, sending bots on patrol or placing turrets on new locations.
Well, these things are the most important changes. If you had an opinion about them, please comment!