I think I'm going to like this system myself. In FO3 it was way too easy to turn your character into a demi-god with 100's in all skills, between all the books and the bobbleheads. Here, we're going to have to really think about where we want to spend those skill points when we level up. Also, you can't just rule out the skill-point only perks any more.
Personally, I enjoyed how it was in FO3. Then you at least had the option of not using the skill books/bobbleheads. Now I find my skill points are always going to Repair/Lockpick/Science, and I'm struggling to get Guns/Medicine/Speech. Even with dump skills (Energy Weapons, Melee Weapons, Unarmed), I'm still struggling to get what I want. Also, there are so many perks, I now really have to debate what to take. Yes, it leads to more specialized characters, but at the same point, it feels like now I have to focus so much on the important items (Lockpick/Science at least) that other useful skills are completely getting left out. With a 9 Int and the Educated type perk, I'm still only getting about 17 skill points per level. So that's 5 levels to increase my Lockpick/science to the next threshold... and that's leaving 7 skill points for other skills. I can't imagine if my INT was less than 9.
Assuming I split the skill points evenly and gave 8 to each skill, it'd take 4 levels to reach the next threshold, and that'd leave no skill points for anything else. Yes, there are skill magazines, but you can only benefit from 1 at a time, and even then, it'll still take as many levels to raise them a threshold because I'd be planning on using one when needed. Combine that with how early you find things that need higher skills and it becomes a pain.
Don't get me wrong, I'm still enjoying the game, but it's rough at times.