By putting skills back I don't mean just create a menu with the skills in it, I mean we also have to tie all of those skills into the main character, world and dialogue.
We have to make it so we get a specific number of skill points per level, probably associated with the Intelligence value of the main character.
We have to edit pretty much everything in the game, combat will have to be influenced by weapon skills (melee, unarmed, guns, explosives, energy weapons) not only for the main character but for every NPC and enemy too.
Chems and medicine will have to be edited to work depending on the medicine skill, dialogue will have to be edited to take into account pretty much every skill (if the Main Character talks about guns, there should be a skill check related to his/her skill value, same goes for every other skill) but in particular the speech and barter skills. Vendors will have to be edited to work depending on the barter skill, Food items will have to be edited to take into account survival skill, sneak will have to be totally reworked so it is dependent on the sneak skill, all the locks and terminals will have to be reworked to be dependent on the Lockpick and Science skills, crafting will have to be reworked to be dependent on the repair, science, survival skills. Everything in the game that requires the player to repair something will have to be dependent on the repair skill.
Perks will have to be reworked to be dependent on skills.
Skills will also have to be dependent on the SPECIAL values.
These are
only a few of the things that
just implementing skills into Fallout 4 would require modders to work on and it would involve editing pretty much every aspect of the game, it would take a lot of time (probably years) to be done.
Now imagine that just for skills, then having to make traits, totally overhaul the perks, totally overhaul the dialogue, probably making an "alternate start" type of mod to replace the tutorial and who knows what else needs to be edited and/or made from scratch in addition to all of that.
There is a lot of work behind the scenes that most people have no idea needs to be done even for what looks like "simple" things

.