I'm going to have to agree with Piecewise, but for the wrong reasons.
The aim of videogames, I think, is to entertain the user. Literally nothing else matters, but it's a tricky business as since there's actual interaction between the player and the medium, the experience is much more personal. What I feel that Piecewise is getting at are the abstractions that make the game less personal, where the game loses touch with the actions of the player versus the skills of his player character, breaking the experience and reducing the 'entertainment' factor if you will.
Now, downright saying that 'point allocation' or 'training based' systems are inferior or superior to eachother also seems fallacious to me. The personal skill of the game developers is what matters most, being able to shape the gameworld to perfectly enclose the player in, and entertain them, is all a matter of the quality of it's design.
So, with this information in mind, it's important to keep in mind that all people have different priorities when it comes to the brand of entertainment that they find themselves most entertained by. This is hugely subjective, and so that saying that any one way of enjoying oneself is superior to another is folly.
This is just a longwinded opening, meant to secure in mind that it isn't method of design that determines entertainment quality, but the skill in design. Now, to my actual point.
I too also think that the way that Fallout 3 and New Vegas treats the player, having played them both, is rather ham-handed. If the game has to slap your hands away from an action you want to do, something has gone terribly wrong. It was always in my opinion that menial tasks, like the 'hopping' example in Oblivion, were so short-sighted that they should not have been included in the first place, and so in order to make a 'training based' skill system, optimally, in my opinion, you'd be forced to limit the things that the character can train in, and also to make the world more apt to reply to the player's decisions.
What I mean by this:
What I mean by limiting what the player can do is simple, things like baking, lockpicking, jumping, or whathaveyou, are skills so mundane that is it not adding 'entertainment value' to allow a player to become a master baker, or lockpicker, or High-jumper. If I may reference the game Deus Ex: Invisible War, where lockpicking is a matter of having enough multitools, regardless of the player's station or experience. Baking is a matter of having the correct ingredients in the correct proportions. Jumping is a matter of not being overly burdened, plus any form of enhancement that would allow an ordinary man to jump higher than normal, like special shoes or magic, or being on a trampoline. Things that the player is apt to do frequently and vigorously, like combat, are those things that most deserve a training based system. A game where a player can use maces, spears, fists, or sword, and gets better by practice, is a straightforward reward to allowing a player to use the weapon they like, and having them get better at it. It also doesn't seem unreasonable to be training "like" skills while training a single one; for example, if a player's character spends most of his time in sword melee, then he is not only training his sword skill, but his strength and experience in melee combat in general. So if there ever comes a day that should he find himself taken with the urge to wield an axe, or mace, he will find that since it pertains to melee as well, he can pick it up with proficiency without having to practice with it for a long period of time like he did the sword. It is in the game designer's hands to make the combat system visceral and immersive, and thus entertaining.
Now, about making the gameworld more apt to respond to the player's decisions. Say that you don't have enough multitools to unlock the magical Hatamaran, it seems more than reasonable to allow you to bust down the door provided the correct tools, even if it is more difficult or expend other resources at your disposal. Or let's say that it's a chest locked by magical means and can't be opened with force, then it might seem more than reasonable to carry the damn thing and chuck it at enemies, until you find a way to open it and extract the hopefully delicious contents. What I'm saying is, that a game shouldn't box you into a clearcut way of thinking, that there should be some leeway when designing the game so that even people that aren't 100% completionists don't feel that they are being left out on content.
I hope that my point has been clear.
And I wouldn't mind there being a bunch of readable books in Fallout 3. Even the ones that weren't ruined couldn't be read, and I always felt I was missing out. Even if it was useless information, I'd have liked to know if that scorched book had atleast a few lines of legible text remaining.