So with the many changes the new installment brings, I feel as if some were arbitrary, or trying too hard to "innovate". Skills were a core mechanic of the fallout series, and a way to raise your numerical stats, such as how much AID items heal you, weapon damage, how hard you are to detect, etc... while perks allowed you to gain new abilities, ways to play and approach various in-game situations. Such as, special dialogue with those of the opposite gender, getting bonus damage resistance when sprinting, being able to tackle flash step to enemies when in melee VATS, etc... In fallout 4, skills have been condensed into the perk tree and this causes a couple of issues with me.
1) The condensed system creates a bunch of "fluff" perks. Rifleman, Commando, Gunslinger, Medic, Sneak, etc... What was the point of removing the skill system if you were basically going to re-integrate what they do anyways?
2) This ties in with #1, since everything is in your perk chart now, you are forced to choose between upgrading your numerical values (the boring stuff), or giving your character new options and abilities at their disposal, which is the whole point of perks.
3) Various skill specialties and playstyles players had at their disposal are now level gated. Want to be an awesome master of stealth to get the drop on your enemies or avoid them entirely to make up for your relative low level frailness? Well you got to wait until level 28. Want to be a brawling machine that only needs his fists to deal with things? Well you have to wait until 31 to maximize your unarmed damage.
The only objectively good change with the new perk system is that the hacking and lock picking skills are now in the binary system (you either have it or you don't).
https://www.youtube.com/watch?v=zLptDJdI0L8 (I highly recommend watching before discussing.)