"Agility is a measure of your overall finesse and reflexes. It affects the number of Action Points in V.A.T.S. and your ability to sneak."
One point of Agility gives you ten Action Points and makes it easier to sneak, which makes it one of the best SPECIAL Attributes on its own merits. Fortunately, it's also got some of the best perks, too, so you've got plenty of incentive to invest in Agility. If you like V.A.T.S. (and if you want to make use of Concentrated Fire and critical hits, you'll like V.A.T.S.), Agility is one of the few attributes you need to pay special attention to.
Like pistols? Then this perk is for you. Like most weapon perks, this one has five ranks, each of which give you a +20% bonus to damage with non-automatic pistols, and the fifth rank also has a chance to disarm and cripple. Nifty enough, so what about the actual weapons, which will determine how useful this perk is? Fortunately, pistols are fairly strong in Fallout 4, including the .44 Pistol and the Fallout-favorite Alien Blaster. You'll also likely make plenty of use out of Pipe Pistols and 10mm Pistols early in the game, which are functional enough. And of course there are also Laser and Plasma Pistols to make use of, which are virtually indistinguishable from rifles in short-to-mid-range performance. If there's one gripe about pistols, it's that there's obviously no equivalent of a sniper rifle, so all in all they have somewhat less long-range utility than non-automatic rifles. Still, if you dig pistols, this is a must-have perk.
Automatic weapons in Fallout 4 excel at two things: dishing out an unbelievable amount of damage in a short amount of time, and wasting your ammo. Like most weapon perks, this one follows the standard five-rank policy, boosting your damage up to 100% (20% per rank) and increasing stagger chance at rank five. In close quarters, nothing will kill faster than a powerful, modded automatic weapon. Of course, kick-back will quickly limit effective range so as to make even mid-range combat less efficient than just using non-automatic rifles and pistols, and ultimately, automatic weapons just aren't as useful in as many situations as non-automatic weapons. They also waste a lot of ammo, as mentioned earlier, making them far more expensive to use regularly.
Ah, sneak... If you want to pop enemies for lovely damage multipliers, you're going to need to sneak up on them, or at least near them. Now that Fallout 4 has competent gunplay outside of V.A.T.S., it's much easier to sneak-kill foes from great ranges, but once you fire, everything near the victim (and perhaps the victim itself) will be looking for you. A higher sneak score allows you to get closer before you take a shot, and become hidden quicker and easier afterwards. If you fancy a stealth build (and you should, it's just free damage you're leaving on the table if you don't), then you'll want to invest in Sneak. At least in the first four ranks, the fifth rank is rather unnecessary.
Kill sleeping foes! What's not to like? Well, anything about that, really. If they're sleeping, you can probably stealth-kill them easily enough anyway. Fortunately, unlike in Fallout 3, this perk now does more, better things than just killing foes that are already very easy to kill. Each rank will give you a percentage to sneak attack damage with silenced weapons (15%, 30% and 50%). It's a hefty enough boost that if you invest in a stealth build (again, why wouldn't you?) and use ballistic weapons (seriously, most ranged weapons that aren't energy weapons have silencer mods) you'll regularly get this damage boost. Perhaps not a first-tier perk worthy of investment, but as your levels climb, it's worth looking at, if it fits your play-style.
Action Boy/Action Girl
You'll get a +25% boost to your Action Ponit regeneration rate per rank of this perk (originally two ranks in the base game, but a third rank was added for the Far Harbor DLC). A great perk for all those V.A.T.S. junkies out there.
The first two ranks give you +25 Damage Resistance and Energy Resistance, but only while sprinting, while the third rank makes sprinting cost half as much Action Points. Looks like even the mighty Agility tree has fail perks. First, +25 Damage Resistance (or +50 with two ranks) is fairly paltry, especially since you only get this bonus while you're sprinting. Unless you're some kind of hardcore melee build, when you're in combat your Action Points are better used, you know, trying to kill things? Dead foes can't hurt you, and while you're firing away in V.A.T.S. you're immune to most damage anyway.
The shadow warrior returns! Ninja massively boosts the damage you deal with sneak attacks, and as pointed out in earlier perks, everybody should aspire to starting fights out with sneak attacks. Again, it's just free damage, there's no reason everybody shouldn't be starting out (and if you're really dedicated to it, finish) most fights with sneak attacks. There's a discussion to be had whether sneak attacks are better with melee weapons or ranged weapons, and this perk goes a long way towards keeping the melee build viable, what with it's x10 damage modifier at rank three. On the other hand, using guns to perform sneak attacks is much easier because of, well, you know, range? Also guns just out-damage most melee weapons considerably. Either way, sneak attacks are good, and this makes your sneak attacks even better, so this is a perk almost everybody should get.
For most guns, reload speed is not a huge issue. You'll reload fast enough without this perk, and the few guns with painful load times (they are very few) tend to compensate with large clip sizes. Pass on this perk.
If you melee, you want this perk, especially if you V.A.T.S. in melee, which you'll certainly want to do once you get this perk. Blitz allows you to engage foes in V.A.T.S. with melee weapons at a range, essentially giving you a short-range teleport attack. This makes it much, much easier to perform sneak attacks with melee weapons, and is almost essential for a potent melee build. Given that melee builds themselves are somewhat questionable, however, well, it's a perk that most people won't need on account of just using superior ranged weaponry. Still, doing that whole blitz-ninja thing with a good melee weapon and a x10 sneak attack multiplier is something else.
The first rank of Gun-Fu give you a 25% bonus damage to the second target (and beyond) you aim at in V.A.T.S, while the second rank gives a +50% bonus to the third target (and beyond). The third rank makes all hits count as critical hits to the fourth target (and beyond). Obviously, the power of this perk is based on a few things, one of which you can control, the other you cannot. If you have a V.A.T.S.-based build and are committed to wearing armor that increases your Action Point and using low Action Point cost weapons, this perk will do wonders. The more shots you can get off in V.A.T.S., the more people you can target, the more bonus damage you'll score. With the right gear, a Combat Rifle or Laser Rifle can easily score over ten shots per Action Point bar, which will make this perk do wonders.
The other part of the equation, however, is enemy density, which you can't control, and honestly, it's not uncommon for you to be facing off against three or four foes. Of course, with a stealth build you'll try to keep some distance, limit exposure and pick foes off, which doesn't always synergize with this perk well. There are also many times when there are only one or two foes around (or in sight), at which point this perk will be of somewhat limited value. Also there's the fact that Concentrated Fire rewards you for focusing your shots, and Gun-Fu ramps up damage as you spread things around. That's not to say with 10+ shots in V.A.T.S. you can't get both adding to the cause, but it's often better to eliminate one foe quickly in V.A.T.S., which triggers Grim Reaper's Sprint and lets you immediately target another foe, something which Concentrated Fire is more adept at doing. And no, if you have four targets on screen at once and take one shot at #1, one at #2, #3, #4, then take a second shot at #1, that second shot at #1 will not get the same bonuses you got from shooting at targets #2, #3 and #4, so you'll need to spend a good bit of time in V.A.T.S. picking starting shots against the weakest foes so your later shots against the strongest will pack the most punch.
All in all, the damage output is nice, and if you plan to make use of this perk, the pain of having to boost up Agility isn't exactly much of a burden to bear, given that it's an Action Point based perk. But you'll frequently be limited by the number of enemies on screen at a time, and the V.A.T.S. fidgeting you'll have to do to get the most out of your Action Point bar does get tedious and leave you vulnerable. A very potent perk for the right build, but since it doesn't synergize as well as others, it's not quite at the top of the pile.