I respectfully disagree with the above assessment. If you used all of your perk points towards your SPECIAL stats, you'd spend 40+ levels just on stats. You wouldn't gain any of the damage perks, sneak, lockpick, hacking, etc. So while you are correct that you can make a character with 10 in all of the SPECIAL stats, you only gain limited benefit from doing so. You gain much more efficacy by using the perk points on actual points, and only taking SPECIAL upgrades when you want to reach a certain perk you can't gain with what you have now.
On the topic at large, I can kinda understand what people are talking about by losing the 0-100 points in skills. With skill books and other aids, you can use fewer points at a level up to reach a certain threshold for skills. And some people feel a higher sense of achievement when their skills are going up, however slowly or quickly they wish, rather than just one point that gives you the benefit of that skill. They also get the freedom to spend those points how they wish, even if it doesn't matter in the grand scheme of things, with the 25/50/75/100 point milestones for the skills to actually do anything relevant. It's very similar to how people reacted when Bioware changed the skill trees between Mass Effect 1 and ME 2&3.
I personally like the new system, even though I liked the old skill system. Now, I feel I have more freedom to choose how I want to specialize my character, with the ability to gain a couple of SPECIAL points to unlock certain perks, while at the same time I feel like each perk I choose is an important decision to make. We only get one point per level, and even if levels come fairly quickly at first, you still need to decide if you want to pick that lock you found a town or two back, or if you want to hack this terminal here, or if you want to take a dip into a highly irradiated pool, or if you really need just that little bit extra damage to fight the Radscorpions over the next hill. Add the weapon modification system to the perk system, and you really have a setup that adds a lot of subtly to the game while making each choice feel important.
Yeah, I agree the balancing could use some tweaking, but the system as a whole has my enthusiastic, unfettered approval. I really wish those who dislike it could see it from that viewpoint, although i respect their opinions.