They're going to make building your character such a nuisance. If the SPECIAL spread you chose at the start of the game was the sole means of determining which perks you could acquire, and SPECIAL bobbleheads only raised their respective attribute bonuses, then we could just focus on exploration and not have to plan a bobblehead collection route to make our builds work.
They're not a problem if you're going to max out a certain attribute anyway, but the trouble starts with attributes which you only need to raise for the perks themselves, and not the bonuses (ie. if you don't want to use VATS, then perception is useless. If you don't want to use VATS or sneak, agility is useless. If you're going be a sociopathic loner, then charisma is useless); if you pump an attribute just enough to grab a certain perk, then essentially you've just wasted a level.
Of course, I could just ignore bobbleheads altogether, as I did in FO3. That's probably what I'll end up doing, but it's disappointing. I feel bad for those guys who will compulsively but begrudgingly head for the INT bobblehead at the start of every single game to max out their XP gain. I know them well, from my time playing NV .