I found the bobble heads adding to the player's stats contributed to how easy it was to become way too OP in Fallout 3, resulting in all of your skills being max, with about only two or three being at least 80.
I wouldn't mind bobble heads returning, but I believe they should work differently. They should continue with having a bobble head for each skill, but instead of stat increases, they should grant certain effects for that skill instead and you can only have one active at a time. Think of the standing stones in Skyrim, only this time they're just the bobble heads of Fallout 3 and are still specific to certain skills. Of course, these effects shouldn't be anything too significant. Just some passive effects I'd say. No granting abilities to call in a random nuke with the explosives bobble head. More like higher percentage chance to stun or knock back enemies in an explosion.
You'll be able to switch out between them at whatever location they're stored at (ex: Megaton house, Tenpenny suite).