The problem with mixing a first-person shooter with a role-playing game is that they are, basically, as diametrically opposed as two genres can get. The cornerstone of an FPS is in the feel of its gunplay and player movement; the questions players subconsciously ask themselves while playing are: how does shooting feel? How accurate are the weapons and are the bullet spray, recoil, and weapon damage consistent with what a player would expect from the weapon? Is weapon behavior relatively reliable? Are the player's skills in targeting his own or is the game modifying them to an unexpected degree? A first-person shooter places the gamer at the helm of the game; the more a player feels like he/she is in charge of his in-game avatar, the better. With this preconception at the forefront of the game experience, players enter into a game world with expected grounded in their reality and expect somewhat realistic or reliable behavior. Shooters that have unrealistically-behaving real-world weapons will seem immediately "off" to any gamer whether he has real-life weapon experience or not; a shotgun which behaves like a sniper rifle will seem strange to anyone while a sniper rifle that has a large box of possible inaccuracy around a gamer's targeting reticule will be a source of future gamer rage-quitting.
At the other end of the gaming spectrum are the more measured and cerebral gaming experiences found in role-playing games. The genre is practically defined by its prolific character building design that has a player's character(s) advance in level through experience points achieved in various battles. With every level, a character's stats increase and this, in turn, makes him more powerful. The original Black Isle-developed Fallout games are no exception to this as all of the combat encounters in the games were handled as turn-based affairs steeped in a player's allocation of action points.
These are, as can be expected, game designs that are inherently at odds with each other.
Bethesda managed it, though. Much to the chagrin of the world's mutants, the death of super-mutants in Fallout 3 is handled in a way that is not only consistent with the original duo of games but manages to be a fun setpiece of Fallout 3 throughout the entirety of the game. The mechanic is introduced to denizens of Vault 101 as the Vault-Tech Assisted Targeting System (V.A.T.S.) and served as a time-independent targeting system to aid a player in blowing off specific enemy limbs (screenshots below). When the player is ready to shoot something a mere button is pressed and the game enters its targeting mode and the player can queue up body parts to shoot and once the sleection is finished the game goes into a stylized camera that depicts the macabre explosion of blood, organs, and limbs in slow-motion. Once the process is done the player is, most likely, out of action points to spend on V.A.T.S. targeting and is forced to rely on his skills as an FPS gamer to finish off remaining enemies or find cover until his action points have recharged enough to allow for more V.A.T.S. shots.
V.A.T.S. at times seems like little more than a compromise made for RPG-minded gamers to eliminate traditional skill-based first-person shooter mechanics (which would make Fallout 3 more shooter than RPG). It does give the player a seemingly unfair advantage in the game world; when I had the opportunity to use VATS on any enemy in the game, save for one boss-like encounter, I always had the upper hand and, what's more, rarely took more than a shot or two while my character performed my V.A.T.S.-dictated actions. This mode of combat appears to give players a very high likelihood of both critical hits and, in some instances, a separate timeline than the one enemies were acting on when V.A.T.S. was used in combat as opposed to an entirely real-time encounter. It's also a greatly more effective form of combat than choosing to avoid the use of V.A.T.S. throughout the entire game and rely on the game's somewhat flawed implementation of traditional first-person shooter mechanics. Bethesda avoids the pitfalls of past hybrid games in that, for the most part, what a player points and shoots at with any decent gun in the game is reliably hit but the feedback the player receives for a successful hit is vastly inferior to the kind of feedback that V.A.T.S. provides with its slow-motion gory cinema of death.
The faults of the real-time combat in Fallout 3 really don't matter. The blend of V.A.T.S and real-time shooting is what Fallout 3 seems made for and, when that path of play is chosen the game's combat shines in a way that I never thought would be possible. In fact, the game positively revels in its existence as both a real-time shooter and pseudo-turn-based RPG game because, when played the way that Bethesda seems to encourage, Fallout 3 manages to feel like a Fallout game.