So, one thing that's always bugged me has been the comparative lack of perks available. To that end, I've come up with (or adapted) a whole bunch of them for use. Obviously, nopony has to use all of them, or any at all. I'll just put the a bunch of them here for anypony that's interested, and because the sheet I'm recording them on has several that are designed specifically for the Group 2 rules, and will not fit with other rules. A fair few of them are simply adapted from existing Fallout 3 and New Vegas perks, but I'll include them anyway.
Level 2
Fascinated Foal: The way things work have always filled you with a sense of wonder. You gain an additional five points to your Science and Medicine skills to reflect your studies into the subject. You may take this perk up to three times.
Other requirements: 4 INT
Friend of the Night: Truly, you are Luna’s disciple, and you’ve spent enough time in the dark that your eyes have gotten very good at adjusting to give you much better night vision than most other ponies. You gain a natural night vision that reduces all penalties for actions attempted during low-light conditions by ten points, and can even negate the penalty entirely.
Other requirements: 6 PER, 30 Stealth
Gun Nut: Your dedication is clear, and it shows in your skills. You gain an additional five points to your Guns and Mechanics skills. You may take this perk up to three times.
Other requirements: 4 INT, 4 AGI
Heave, Ho!: You can really chuck something, if you want to. Objects you throw will travel as much as 50% further, and get there faster.
Other requirements: 5 STR, 30 Explosives or 30 Melee Weapons
Li’l Leaguer: Hours spent practicing for the hoofball team while you were younger means you know your way around a ball and bat. You gain five points in both your Explosives and Melee Weapons skills. You may take this perk up to three times.
Other requirements: 4 STR
Rapid Reloading: You can swap out a magazine or revolver cylinder faster than anypony you know. All reloading costs are reduced by 5 AP.
Other requirements: 5 AGI, 30 Guns
Theif: You know how to get in and out of somepony’s pockets, and their house. You gain an additional five points to your Lockpick and Stealth skills. You may take this perk up to three times.
Other requirements: 4 PER, 4 AGI
Level 4
Horse Whisperer: Ponies just understand what you mean and see what you’re trying to say very easily. You gain an additional five points of Speech and Barter.
Other requirements: 4 CHA
Pathfinder: You know you way around the woods, that’s for sure. When reading maps, you gain an equivalent of twenty points of Survival.
Other requirements: INT 4
Rad Pony: Time spent in the irradiated wasteland has given you a limited regenerative quality when you’re irradiated. Your (un)natural healing rate is increased by one point per hour resting and two points per hours sleeping.
Other requirements: Survival 70
Scoundrel: Somewhere along the line, you learned how to really talk. You gain an additional five points to both Speech and Barter. You may take this perk up to three times.
Other requirements: 4 CHA
Level 6
Herd Rage: You stand up for your friends, especially if they’re hurt. Pick a party member. Whenever that party member drops below 50% Overall Health, you take half damage from all sources. The party member you pick must accept before any advantage is given. You may take this perk as many times as there are members in the party. If one target of this perk leaves the party or is killed, you may pick a new one, so long as they also accept. You may not pick yourself. This effect does not stack.
Other requirements: 6 CHA
Fortune Finder: You’ve just got a kind of luck about you. You find more bottlecaps in containers than you normally would, equivalent to your Luck in d10s whenever bottlecaps are found.
Other requirements: 5 LCK
Gunslinger: Pistols and smaller weapons are just how you do business. On account of your familiarity, you gain a ten point bonus to hit with pistols and one-armed ranged weapons.
Lead Belly: For whatever reason, your body is exceptionally resistant to ingested radiation. You only receive half the normal rads when eating or drinking irradiated food or drink.
Other requirements: 5 END or 40 Survival
Professional: When a pony isn’t expecting it, you know where it hurts the most. Whenever you make a sneak attack against an enemy with a one-armed weapon, you gain an additional 2d10 damage after figuring critical damage.
Other requirements: 70 Sneak
Shotgun Surgeon: Your shotgun skills are as sharp as a scalpel, and just as good as laying a pony open. Regardless of ammunition used, you ignore up to 10 points of enemy Damage Threshold when wielding shotguns.
Other requirements: 45 Guns
Level 8
Commando: Shoulders up, eyes open. Time spent practicing with rifles of all kinds grants you a ten point bonus to hit with rifles and other “two armed” weapons.
Impartial Mediation: Your thoughts are clear and your speech pure. When you have karma between -10 and 10, you gain a bonus of twenty points to your Speech skill.
Other requirements: 5 CHA
Living Anatomy: A practiced eye can spot many things. In combat, you can easily spot how much overall health an enemy has, as well as their damage threshold.
Other requirements: 70 Medicine
Scrounger: You find ammunition about as often as you find dust bunnies. Whenever you find ammunition, you find additional ammunition equal to twice your Luck plus 2d10 percent, for a maximum of 40 percent more.
Other requirements: 5 LCK
Stone Wall: You are a mountain among ponies. Against Melee and Unarmed weapons, you gain an additional five Damage Threshold and are not knocked down on critical hits.
Other requirements: 6 STR, 6 END
Earth Pony specific perks
Level 2
Earth Pony Reliability: A weapon you’ve gotten your hooves on is practically a charmed thing. with your deft hoofwork, you can repair a weapon or armor to 120 percent quality. This does not affect the price or qualities of the weapon or armor beyond making it more durable.
Other requirements: 50 Mechanics
Level 4
Ingenuity: Being an Earth Pony means you can see how things could be made better just by looking, and with the proper know-how, you can actually do it. With the aid of some tools, you can take like weapons or armor and combine them, using the best parts of each to make the resulting product even better. You may only combine like items, and the maximum bonus cannot exceed an additional five damage or an additional five damage threshold.
Other requirements: 4 INT, 75 Mechanics
Entrepreneurial Spirit: You might be able to take the pony out of civilization, but you can’t take the civilization out of the pony. Your refined sense of business means you can sell clouds to Pegasi. When selling equipment, you gain an additional 20 points to your Barter skill.
Other requirements: 4 CHA
Pegasus species perks
Level 2
Used to Crashing: Any Pegasus that’s flown for any real length of time crashes pretty frequently. It’s no mark of shame when it happens, either. You’ve crashed more often than most, and as a result, you know how to land to avoid hurting yourself. During a crash landing, you take half the damage you normally would.
Other requirements: 4 AGI, 30 Flight
Birds of a Feather: You know how your kind works. Attacks against other Pegasi or Griffons deal an additional 1d10 damage. When in conversation with your winged brethren, you unlock unique dialogue options.
Level 4
Not a Clay Pigeon: It’s no longer open season. Against any attack made by shotguns or scatter weapons behave as if you had a damage threshold five points higher. Slug ammunition ignores this perk.
Other requirements: 5 AGI
Griffon species perks
Level 2
Crash Course: In flight, you can choose to intercept another flying character and divert them, roughly, to the ground. Normally, this deals full crash damage, but you know how to take somepony out of the air. You only take half crash damage from the impact, while your target takes full.
Other requirements: 4 PER
Pegasus/Griffon/Alicorn shared perks
Level 6
Stonewings: No more clipped wings for this flier! Your wings immediately gain a permanent 50% bonus to your wing limb health, but you are still unable to fly if one or both wings become crippled.
Other requirements: 5 END
The Little Birdie That Could: You know where you need to be, and nothing at all is going to stop you. Even if you have a crippled wing, but not two, you can still fly at half your normal speed. Every turn spent airborne costs you 1d5 Overall Health. This kind of flying cannot be sustained for long periods of time, and may only be used during combat.
Other requirements: 6 END
Level 10
Keep on Flying: Pain in your wings doesn’t even make you flinch anymore. Your wings take 50% less damage from all sources (DR 50). Your Overall Health is still affected normally.
Other requirements: 6 END
Still obviously a work in progress, but variety is the spice of life.