I think Bethesda should implement a system of Skill Point refunds for both the Fallout and Elder Scrolls franchises. Meaning, that if you develop a skill to 100, and then find skill books for that maxed out skill, you should be given skill points free to distribute elsewhere.
I was playing Fallout: New Vegas, and had maxed out several of my skills before playing Dead Money. I would allocate skill points into a skill, stopping at 84, and use the 4 skill books (with the Comprehension perk) to max out that skill at 100, without wasting any points by going over. (Also, I just want to point out that I did not wait until a skill was 84 to use the skill books - if I found 1 earlier, then I would level it to 88, and so on.)
Then Dead Money provided an additional skill book for each skill, but I hadn't planned on that. Most of those skill books were worthless to me. Its not a serious problem, but just a small something to improve on.
Besides, since you lose all of your equipment at Dead Money's beginning, I don't want to level my Lockpick/Science to 96, and miss out on lots of containers/areas until I find their appropriate skill books in the Villa / Sierra Madre, or hope to luck out and find the right magazine in time.

In Dead Money, I can understand you missing a few containers and terminals but after beating it, you should be prepared for the next time, since you know what the lockpick and science requirements are.

Second, your idea would defeat the whole purpose of individual skill books. In reality, one book will not tell you everything you need to know about every skill. Ex: Dean's Electronics, repair originally, but now it can allow skill points into guns or survival, it doesn't make sense.

Plus with the soon to come level 50 level cap, you should be able to max out alot if not all skills.

Yes I also thought about that, but now I just collect the skill books I don't need anymore. Besides when you reach lv. 40 there aren't much skills left to be upgraded.

Concerning the sense of the whole idea, I see how an unrelated skill book shouldn't add more skill points to be used on anything. My solution is a bit of a loophole. It is that you are being refunded the indiscriminate skill points provided by leveling up, and are replacing those with the skill points from the provided skill book. Either way, the skill points are the same. But that would be the idea behind the logic.
I just don't want to have a 96 in most skills until I complete Dead Money, then return to the Villa to open a few lockers, chests, and terminals with my new 100 Lockpick and Science.
Like, I said before, it isn't a huge fault with the game. Its just an idea, and I would like to hear other suggestions.

A mind is a terrible thing to waste. And Skill Books feed your mind.