Perks and what to choose. Ask 10 different agents and get 10 different answers, of course, tho there are some similarities. Common choices for the core of the perk set are Black Ops and Assassin, with some Infantry thrown in. Genius 2 is also popular for the regain nano perk action.
For AI perks, the discussion seems to be between Made and Champion of Heavy Artillery. At various points in our careers, a lot of us have perked Enhance DNA or First Aid to equip stuff, usually not as a permanent perkline. Many agents (and other people) also end up training exp perklines Explorer and Training Seminar too, to make SKing somewhat less tedious.
(And because I am afraid of being too much of a grump, I won't point out that this question is asked (and answered) over and over again: recently. . . the thread called "Perks" discusses AI perks, and the threads "Normal Perks" and "New Agent Needs Perk Help" discuss perks more generally. But i won't mention that. *hushes up*)
A very handy tool for planning perks is AODB's perk configurator. It lets you allocate different numbers of perk points to different lines, and see what the net result would be. And of course it links to detailed descriptions of the different perk specials, too, so you can get a good idea of what to expect if you spend your perk points in a particular way.
Some perklines to consider (links to fully perked):
Assassin (10)
Assassin adds 25 Rifle, 100 AS, some evades, and gives a 2% crit bonus. Lovely mods. Assassin's specials are great too: Tranquilizer is a nice snare with a small DD (1012 at perk level 10), Concussive Shot is a nice DD and stun. Toxic shock adds damage for a little while (200/hit for me), and Assassinate is a nice big DD (8-16k+) that requires timing but can make the end of the fight faster. Totally crucial perk line.
Black Ops (10)
Black Ops adds 55 Rifle, 65 AS (and 100 Fling!) and gives a 1% critical bonus. Soften Up is a nice AC debuff and snare, and (tho opinions vary on this next part) Death Strike is a nice big DD (8-16k+ like Assassinate, above) if you can time it right; it requires stun to work - so Concussive Shot or Tumulten are handy and it's not usable on bosses. Pin Point Strike can get to 4-7k as a DD if you have APS (infantry perk special) and Soften Up both running. Chaotic Modulation is theoretically useful for finding AC holes or against a target with armor vs. your damage type. Love this perk line.
Made (10)
Made adds 51 AS and some evades and Sharp Objects. It adds to nano pool and reduces nano cost 2%. I like the specials, but opinions differ. Recalibrate is a 30s boost to Ranged Init, useful for squeezing an extra shot into an AC/GW. Silent Plague is a DoT that scales with perk level. I have Made 9 now and it's 5 ticks at 1000 each for me. The Shot is the big DD payoff at Made 10; I don't have it yet, but on paper, it's 6.5-8k DD with 60s recharge. Lovely :)
Champion of Heavy Artillery (10)
Champion of Heavy Artillery adds 100 Rifle. Nice!! I don't know how the specials are in actual use, since i haven't trained this line yet, but they sound okay on paper: 2800-3840 damage at perk level 10 for Fuzz, and a small DD and moderate DoT from Fire Frenzy.
Infantry (10)
Not a lot of people i know have this trained all the way to 10. If you do, tho you get 120 rifle (*drool*), 20 fling and 400 Max Health. Called Shot (at Infantry 10) is a small DD and DoT. Armor Piercing Shot/Find the Flaw gives a lowish DD of 1500 or so. APS executes super slow for me. I'm working my way up to 10 in this now for the rifle bonus.
Infantry (5)
At infantry 5 you only get 40 rifle, 6 fling and 111 Max Health, but you still get APS and FtF so a lot of people stop here until they have perk points to spare.
Genius (2)
Genius 2 adds 20 to int/psych and a teensy 60 to nano pool, but the Regain Nano special is groovy. It gives 1000 nano (5 ticks at 200 each) every 2 minutes. I love this special. I am in perma-mimic tho; your mileage may vary. Training Genius 3 adds 20 *more* int/psych and 60 more nanopool. I had this trained for a while when i was starting mimics; i untrained it (the level 3 of the perk) a little while ago.
Shadowsneak (10)
Shadowsneak adds 10 AS (yes, 10), 55 sense, and 100 conceal. Night Killer is a DD special that requires an Advy special (Shadow Killer) to run. bleh. I didn't perk this line, so I don't know how the Fade Armor->Shadow Bullet combination works out in practice. On paper, Fade Armor is an AC debuff and Shadow Bullet is a lowish DD. Not a lot to recommend this line.
Sharpshooter (6)
Sharpshooter adds 30 AS and gives a 3% crit increase. Snipe Shot 1 is a lowish (1200-2300) DD, Snipe Shot 2 is a larger DD but requires a soldier perk (Triangulate Target) to be running for you to use it. People who perk this usually do it for the critical increase.
Training Seminar (4)
Training all 4 of these is a +7% exp bonus. That's it. Makes the number of hecklers to kill pre-220 somewhat smaller.
Explorer (4)
Training all 4 of these gives 5% exp bonus. You also get two nice self-teleports that you can use even in SL.
Apparently, we can also train Power Up to 5, and Nano Doctorate to 7. But i don't know enough about these to comment. (And sorry about the order of these; it seemed to make sense at the time.)
So overall, as an "average" agent, you can't go too far wrong with Assassin/Black Ops. Throw in a little Infantry, and Genius when you start to mimic. If you want the 3% crit bonus and have the extra points, you can train Sharpshooter, too. AI-wise, I like Made, but the 100 Rifle from Champ of Heavy Artillery is really nice too. Some people have mentioned the Genome lines for AI perks too. Steer clear of Shadowsneak. Enhance DNA and First Aid are handy temporary perk lines for equipping stuff. And if you love hecklers, then don't perk Training Seminar or Explorer, or you will see fewer of them en route to enlightenment.
