People get angry about the loss but I have to wonder if they really know what they'd be losing. Fallout 3 went to great lengths to minimize the impact of one's special score. If you consider each score in turn, you come to realize the game was largely designed such that only a few scores are actually even remotely important.
Strength - Like all skills, it offers a 2% bonus to a set of scores for each point invested. It also makes tiny alterations in one's capacity to carry objects. However, given one only gains or loses 10 pounds per point, and there exist perks that offer the equivalent of five points of strength for the purpose of measuring carrying capacity, this one is largely useless.
Perception - It affects when you get red tics on your compass. It thus provides no more information than the player themselves could pick up by paying attention on average.
Endurance - It affords a small bonus to HP per level. This one is almost entirely unless playing the game in an intentionally difficult way using low damage weapons and low protection armor. It also provides some resistance to environmental hazards. That these hazards are either easily avoided or represent such an insignificant threat that they can be ignored combined with the ease of combating the problems associated with them makes endurance useless.
Charisma - Entirely useless in fallout 3 save for the bonus to skills. New Vegas made it somewhat useful by offering buffs to companions based upon this score.
Intelligence - Improves the number of points you get at level up. This skill determines your basic capacity to build your character and thus is the most important skill.
Agility - Useful because it offers bonuses to reload time, movement speed and determines your AP pool. For most, the second most important stat.
Luck - determines base critical hit chance. Usefulness determined by weapon selection as fallout 3 offers a means to easily get a 25% critical chance. New Vegas ups that to 70% with certain weapons, perks and garments.
Fallout 3 demonstrated that it was possible to make four of seven stats functionally useless or, at best only useful in certain capacities. Couple that with the fact that few perks require more than 5 or 6 in a stat to be selected (if they have a requirement at all) and you find that the system doesn't really have an impact. The rational way to play the game is to maximize intelligence and agility and potentially luck.
In contrast, Fallout New Vegas was an attempt to once again make these less useful stats important. Charisma modified companion damage and health. Weapons have a strength requirement and impart severe penalties if you do not meet the threshold. A dramatic increase in the number of environmental hazards you encounter coupled with a tremendous reduction of items like rad away and poison cures mean the bonus resistance against such things given by endurance becomes useful. Furthermore, tying a wider number of checks to these base stats made them important points to consider at character creation.
If we consider the two routes, the abstraction of the system to non-existence (how Skyrim handled it) versus doggedly staying the course like Fallout New Vegas we arrive at the real problem. With New Vegas (and the older Fallout models) the player is asked to make choices in the opening moments of the game that will determine how readily they can play the game in a certain way. They are asked to do this before they've played the game. A choice made blind is no choice at all and thus you rapidly arrive at the real problem. This model requires out of game knowledge of the mechanics governing play and it doesn't take much meddling in this area before role playing is lost to power gaming. There is a correct way to play New Vegas efficiently - that model is high intelligence/luck/agility, with small penalties across strength, and charisma. Any penalty encountered by the creation process can easily be overcome through mechanisms already in the game.
By contrast, Skyrim does not ask the player to make any such choice. They give them a rudimentary set of tools when they start and push them into the world. The choices that govern the growth of the character are made as they play in an organic fashion. It is still possible to play the metagame of course, but at least the first time player is only asked to choose once they have an idea what sort of impact that choice is going to have.
In my view, the superior design choice is simple enough to identify. Any time a choice doesn't matter you don't bother giving it to the player. This is why for example I didn't mind that the skill trees collapsed in Mass Effect 2. There were few moments on any given bar that investing a point offered anything tangible so why have those blocks in between? Likewise, if a choice is important, never ask the player to choose until you've given them the information they need to make an informed decision. Otherwise, it's just chance that they get it right.