This guide is meant to give an overview which perks are in which "tier" (god-tier to garbage-tier). There will be no spoilers other than me mentioning the existence of a late-game.

GOD TIER (in early game, mediocre in mid-game and late-game)

• Survivor - increases maximum hit points (by 20)

You need as many agents as possible early on who have this perk so you can take out any enemy agents in stealth. There are ways around it (breaching and point blank) but they are much harder to pull off - in particular in the beginning.

TIER 1 (every agent wants these)

• Faster Movement - increases movement range (by 1) for EACH movement point
  
• Combat Senses - increases maximum awareness (by 20)
  
• Expert Marksman - single shot attacks no longer end the agents turn (semi/full auto will still end it)
  
• Brickhead - protects from stun effects.

You should try to get those for every agent and I'd choose that order. Additional movement is useful almost every turn for almost all your agents. Expert marksman is useful from the get go and gets even better in later chapters. Max awareness is better than cheaper take-downs or faster regeneration - both in stealth and in combat. A unlucky stun can wipe your whole team - no matter how strong they are otherwise. Stuns come into play late but they are utterly imbalanced.

TIER 2 (good)

• Composure - increases awareness regeneration (by 10)
  
• Fearless - agent cannot be suppressed
  
• Custom Gear - improves reload times. (without specialisation: 1M/1FP => 1FP; 2M/1FP => 1M/1FP; with specialisation: 2M => 1M; 1M => free)
  
• League Pitcher - throwing grenades no longer ends the agents turn

Awareness regeneration is mostly a convenience perk for faster stealth but can be really good. Suppression can get agents killed (in later missions). Reloads can be a pain if they come in a bad moment and grenades are very powerful (and get even better later on).

TIER 3 (nice to have)

• Cold-blooded - decreases cooldown on the Focus ability (by 1 turn)
  
• Paramedic = improves movement range by 2 when carrying an agent. Does not stack with "exertion"
  
• Dancer - decrease awareness cost of dodging (by 5)
  
• Revenant - increases critical timer/ agents take longer to bleed out

All of these are rarely useful but they can come in very handy.

TIER 4 (effect is negligible)

• Scar Tissue - protects from loss of damage threshold caused by corrosive substances
  
• Masochist - improves damage threshold (by 6)
  
• Freediver - protects from harmful effects of gas clouds, except loss of vision
  
• Quick Recovery - increases HP recovery in hideout
  
• Mild Paranoia = improves benefits of full cover. Normal full cover = -75% dmg. Improved = ?80%?
  
• Low Profile = improves benefits from half cover. Normal half cover = -50% dmg. Improved = ?60%?

You should bring healing items on missions so you hardly ever need the infirmary for more than a couple of points. The rest of these perks have too little effect to be chosen voluntarily.

Garbage tier (never take any of these)

• Martial Artist - decreases awareness cost of takedown (by 10)
  
• Actor - reduces the distance at which enemy agents can detect your agent's disguise (by 3 tiles)
  
• Stalker = increases the range of the overwatch cone by 4
  
• Peripheral Vision - overwatch field remains circular in a wider radius (radius increased by 2 tiles)
  
• Vietnam Veteran - increases the width of the overwatch cone
  
• Gifted - bonus (20) XP for missions

Martial artist is worse than max awareness, worse than awareness regen and you have no time pressure in stealth. Actor was nerfed and 3 tiles don't make much of a difference. The problem is that is can hurt your playstyle. You want to avoid being spotted at all cost and relying on a slightly reduced line of sight is simply unnecessary. That being said, if you feel like taking a few avoidable risks to speed things up you might want to upgrade Actor to Tier 3. [Edit: there seems to be an option to change "actor" back to what is was before the nerf: enemy agents cannot see you. I would strongly advise against doing so because it basically breaks the game.]. Overwatch is not how you kill enemies in this game and a bigger overwatch area is hardly ever useful. XP is used to get perks and you can easily play an additional mission to get more XP.

You can get perks from the agents origin. Most of those are inconsequential and would clutter this overview but some are useful.

From my perspective there is a perk that is superior to all others by a huge margin: "Warn Ally". This ability restores ONE HUNDRED awareness of another character and you pay one MOVEMENT point.

Other perks that are good include:

• Heartbeat Sensor: reveal enemies in the area of effect, without having line of sight to them
  
• Lucky Break: The first time the agent receives damage on a mission, they temporarily become able to dodge at no cost
  
• Buckshot: Deals damage to all characters within the conical area of effect

These three are also useful but you can get them from "training" your agents: sure shot, interconnected, eye for talent.

GOD TIER

• Exertion

Situational but those situations WILL come.

TIER 1 (every agent wants these)

• Sure shot

A useful addition to headshots.

TIER 2 (you don't have enough slots for these)

• Interconnected
  
• Blinding Laser

Everything else is not worth your training-slots (at least not for the perk). You want one "pistol"/one-shot slot and one combat slot so there is not a whole lot of leeway...

Apart from all of that you want exactly one agent with "eye for talent" and you should have one long before the corresponding training becomes available.