I don't understand why people have to believe that a game having a FPS view and combat in such a view that requires you to manually aim and fire can never be called an RPG no matter what else is going for it.
An RPG I believe is nothing but a game in which the player "plays the role" of a character who lives his or her own individual life with a unique story that may or may not affect the fictional world. Anything the player wants to do can only be done to the extent to which the character is able.
All adding an FPS component to an RPG game does is make it so the player can literally see things the way the character would. Sure, the player's skill in using cover tactically and aiming a weapon is taken into account, but because of skill checks the weapon, although it may look like it's right on target, will be missing like crazy if the character doesn't have a sufficient amount of skill to use it.
Mass Effect is by far the best example of this RPG-FPS hybrid, and it does not appeal to the stereotypically impatient, action-seeking FPS gamer. It is strictly an RPG with a real time combat system, which is almost entirely limited by your character's gear and skills. Only the use of cover, squad leadership, and grenades/throwables are player skill based.
Now, there's two things Mass Effect does better than Fallout 3, that make ME a better RPG overall than FO3 and FO3 a better "FPS", if you can even call it that, than ME. Combat, of course, and story.
There's are limitless threads about how the FO3 story suffers due to poor dialogue and player/character choices in conversations, lack of open endedness with many invisible walls, etc, so I won't dwell on it here.
The problem with Fallout 3's combat not being RPG-enough is not because of the FPS/TPS combat at all. Nor is there a problem with VATS. The fact that you can use BOTH normal FPS/TPS and VATS at the same time is the issue; in essence, it's like having both active abilities that consume stamina/mana/a round/a turn on top of an "auto attack", and can use them together in the same round of combat.
Imagine blasting a Fireball at an enemy and then slashing them with a greatsword in the same round in DnD. From a player's perspective, all you did was click a few things, but in the character's perspective, he had to conjure this great ball of flame and launch it with enough force at the enemy, and then he runs after his fireball and throws around a huge sword in his chainmail without breaking a sweat. That's like the Matrix on crack.
There's less RPG-style combat (character's skill emphasized over player's skill) when you have more breathing room for character failure due to player-enhanced combat. In DnD if your Lightning Bolt is Evaded or Resisted, that is a major set back because your character's skill/stat checks failed, giving your enemy the upper hand in combat for that round. Your combat abilities are limited by your character's ability, your enemy's ability, and random chance, and every round has the ability to make or break your character.
Instead of being screwed by missing shots in VATS, you can just go into FP view and shoot the person up. Unlike VATS which is limited by AP, FPS mode let's you keep firing without worry (other than easy to reload magazines), allowing you to make up for any shots that miss. In Mass Effect, for comparison's sake, combat is limited by weapon overheating and biotic/engineering cooldowns.
Really, if combat were to be more character based than player based, every shot should require AP and enemies should be rebalanced accordingly. Right now, they seem super easy just because, with VATS + FPS mode, your character has Godly, Neo-on-speed reflexes in the eyes of your enemy or a bystander.
If normal shooting in FPS/TPS mode also required AP, then players that are more comfortable with TB RPG combat can use VATS to simulate the same punch-for-punch idea, and players that are more familiar with FPSs can gun enemies like normal.
Your character's abilities would make a larger difference since you can't really spray and pray due to the AP limitation. In Mass Effect, a soldier type who relies on weaponry won't see overheating weapons too easily due to his/her skill with the weapons, which allows enemies to be dispatched quicker, and can switch to a weapon he is less proficient but still skilled with if his primary weapon is unusable for a little while. An Adept/biotic heavy user on the other hand has to use the crap out of biotics to fight because his pistol, the only weapon he can really use, is going to be very limited in power and overheat quickly due to weaker pistol skills.
Unlike Fallout 3, Mass Effect achieves a nice balance that allows for the character's gear and abilities to outweigh the addition of the player's input in a round of combat, keeping true to RPG combat in an FPS perspective. Were Fallout 3 to have limitations that prevented you from seamlessly switching between VATS and TPS/FPS at will within the same "round of combat", both FPS-style and TB-style combat could exist in a balanced, character-centric fashion.