Gopher posted a link with his take on the skills being converted to perks at https://www.youtube.com/watch?v=VOOz_fHHt0o.
He makes some good points about the skills still being there just hidden and modified by what perks you take.
His point was that converting perks to skills wasn't dumbing down the Fallout skill system but actually improving it by offering more choice.
By using perk skills you can create a better defined character since the perks show what the character is good at better than just having a single skill rating covering everything and it was cleaner to boot.
For example in F3 and FONV, a scientific courier with an 80 in the Science skill is equally good with producing chems, hacking a terminal, working on energy weapons, or discussing quantum string theory.
In Fallout 4 depending on if you take the Computer Wiz or Science perk, you can be an expert in software but useless with the hardware.
A Bounty Hunter with the Cowboy, Gun Nut, Gunslinger, and Commando perks would be better with lever action guns and pistols but not as good with automatic weapons like a grease gun or mini gun.
And since there were a lot of perks that had major impact your character's combat abilities already, moving the skill system to perks just put it all in one place.