So, I know no one cares about my opinion, but I am going to give it anyways.
When it comes to Fallout 4's perk system... I really don't have a problem with it. Ultimately because its basically how Fallout 3/NV worked anyways.
While the 1-100 skill system seemingly grants more control over minute details of a character's stats, the problem with it in action focused games like Fo3, NV, and Fo4, is that the player being so in control over how effective guns are makes the majority of those increases relatively worthless. the .7% increase to weapon damage per point from something like the small guns skill isn't noticeable when most small guns only do like 40 damage to begin with, and even getting leveling up your skill by 20 points only gets you from 40 damage to 45 damage, which isn't that big of a deal, maybe one shot or two less to kill something.
Similarly, when it came to things like hacking/lockpicking, the only ranks of the related skill that mattered was 25/50/75/100, meaning all other were literally worthless, since there was no 35 skill locked lock, or 45 skill locked terminal.
When it came to things like medicine, going from 20 to 40 medicine skill you only gained like +12 hp from stimpacks, but when you had 400+ HP that doesn't mean a whole lot.
Going from these 1-100 skill systems, down to something like a 5 ranked perk, where every rank = 20 skill levels from a previous game, isn't really a reduction of anything IMO, because all those ranks in between didn't really mean much of anything at all, and in some cases, like in lockpicking and hacking, they literally mean nothing at all.
Now the common rebuttal to this is "why didn't they make each rank mean more instead?", and the answer to that is because the skills were already balanced across the 1-100 rank in such a way as the devs felt like getting to 100 made you more powerful, but not so powerful you broke the game(though you often did anyways). Trying to do things like just tacking on more +damage, or +accuracy, or +HP restored, to skills would only make the game even more unbalanced. You can't just add on to something without taking away from another to keep the balance, and ultimately that just ends up with what we got. They kept taking away the minor/worthless bonuses from each individual skill point, and stacking them onto each other, until they came up with a 1-5 perk range where each perk offered a satisfying amount of +whatever.
When it comes to weapon/armor crafting, I find the whole system fun, and theres a lot of options for everything except the really weird weapons like the fatman, where theres really not too much you can mod on it given how simple it is. I do wish there were a few more weapons/armors in the game, but a large problem both Fo3 and NV had was that there was really only about 5-10 weapons/armors worth using at endgame, and everything before you got to the endgame just didn't matter anymore. The modding system we got in Fo4 has kept far more weapons far more viable then in the past games, which is an improvement. But as I said, I do wish there were a few more, especially when it comes to armor. The whole normal -> sturdy -> strengthened -> heavy upgrade thing for armors, where each version adds more pieces to the armor, was a neat idea, but it doesn't really make up for the lack of non power armor in the game.
I generally found the gunplay to be miles better then in past games. Whereas Fo3 and NV were well known as being games where you basically had to use VATs because of how bad the guns were, I found myself almost never using vats in Fallout 4, and not even realizing it, simply because "it just wurks!". Its nothing like the top tier FPSs or anything, but its perfectly fine for the kind of game it is.
The world design was, IMO, some of the best Bethesda has done. Everything was so detailed, and felt so "lived in" that it really felt like a living world. One of my favorite touches was that most of the raider groups with names bosses in them had computer terminals talking about the other raider bosses, and these terminal entries change based on if you have killed that raider boss or not. Another neat thing was that if you sneak around, you can hear raiders talking about the various raider gangs, and their dialogue changes after you kill that gang. Both were neat touches showing the people of the game world reacting a bit to what you did. And the glowing sea was a wonderfully desolate place.
When it comes to the main plot, I found it far better then Fallout 3, if not a little short. I did like how all the faction's questline interacted and weaved together, with you being able to play multiple sides for some time before having to make a choice. It made the whole situation a bit more fun then New Vegas's far more rigid faction system, where 2-3 quests for the other side completely blocked you off from the others forever. And I liked how each faction was roughly equal in ideals, except maybe the Institute were a bit more evil seeming in the long run.
My biggest problem with the game comes largely from the lack of side quests. The few that are there were fun, like the Cabot House questline, the USS Constitution quest, The Silver Shroud, The big dig, etc. etc., but overall, I just didn't find al that many quests in the game. And that's really what kills me about this game. Skyrim had so many daedric quests, 4 guild questlines, the main quest, and a number of side quests, I just cant imagine why this game has so few by comparison, its really is bizarre. I understood it in Fallout 3, since they had to rebuild the engine to support guns, make VATs, and do a bunch of first time scripting for a sci-fi game instead of their standard fantasy, but all of that stuff is already done, and I just don't get why this game has so few. Whats even more bizarre is that looking at the game with Fo4edit shows there were like 6 side quests cut from the game, 4 of them were cut entirely, and another 2 still remain in the game, but totally lack objectives or anything else. I just don't get why so many were cut out.
So that's what? main quests, side quests, crafting, skill system, world design. I think that's most of it really. If I forgot anything really, I'll add it on later.