Okay, so. I think some revisions are in order for some perks, which are either just completely broken (not in a "too good to be here" way, but something that just doesn't work for the system we have now), or just need some clarification on the wording, or adjustments to which I would say they need to be ostensibly better for anyone to take them outside of "roleplay" reasons (which are admittedly completely subjective on my part). As such, I'm going to organize them by what how I see the problem as.
Subjective: This is just my opinion, and typically is just some complaint about how the perk works in the logic behind it, or how it operates based on what I've seen in how it's presented in game. Your mileage may vary.
Wording: Typically, it's just a matter of it being worded oddly where it might cause some arguments between a GM and players on how it works. Somewhat subjective, but typically just nitpicking.
Mechanical: This perk does not make sense in this system. It is intrinsically broken, and is usually a remnant of how it works in the video game not being how it works in the tabletop, or a remnant of the past edition. These typically need to either be removed, or reworked to apply to this game.
Right! Let's get down to it.
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Brown Muzzle: (Level 2, Subjective) I have never seen this picked. Maybe it could do something like the "Sex" perks like Black Stallion or Cherez la Filly for authority figures to make it a bit more enticing?
Thief: (Level 2, Subjective) So, wait. You can't even attempt to pickpocket unless you have this perk? Lame! Personally, I'd go for having a prohibitive penalty to pickpocket-ing like a -30 outside of having this perk. If you have those many ranks in sneak or in "Lack of Fucks" to mitigate the penalty, well, then at that point, you deserve to give no fucks.
Tail Trick: (Level 2, Subjective) This lacks a lot of "crunch" reasons to get it and that makes me a sad icebox. Personally, I think that this is something EP's, or even all ponies should just get with their racial package. It hurts my head to imagine how EP's at least handle explosives or lockpicking or anything that requires deft movement without it. If they want to be a "badass" and use it to shoot mouthguns or fling around explosives, then they can do it with a -2 to their STR for all purposes and use the AP they have naturally in their turn to fling and fire them around. I am positive that Littlepip or Calamity wouldn't feel too outgunned, and it opens up a new, interesting set of perk ideas for everypony.
Running Tackle: (Level 2, Wording/Subjective) So, wait. Can you not sprint, roll to stop, and tackle somepony if you don't have this perk? How come flying tackle is something you just get and don't have to blow a perk on, then? Does this perk also apply to flying tackles? Also, kind of a weird thing, but the trip rules aren't 100% clear. Do you roll an attack with whatever you have on hoof as a thing, and then do the contest of STR+1d10 against AGI+1d10? If so, why wouldn't you simply always use your hind leg and never have to spend more than 15AP on the unarmed thing if unarmed is your thing? How much AP would it take to use the stock of a "rifle" class gun as a melee weapon in this attempt? Does the +2 apply to the "To hit" or the "To trip" roll? When do you trip if the tackle happens on their turn? Do you have to have the AP left over for an unarmed or melee attack to attempt it? Once again, I think this is just something that you should get and have to deal with the penalties for.
Explodey McGee: (Level 4, Subjective) There is absolutely nothing wrong with this perk. I just wanted to take this moment to give props to the folk in question that improved it.
Hit the Deck!: (Level 4, Wording) Aren't all explosives ranged? Now I kind of want to see the elusive melee explosive that this doesn't cover.
Are we talking all weapons that are under the "Thrown/Placed" explosives weapon tag, as well as explosive projectile weapons and the like? If that's the case, do we include stun damage coming from stun grenades and attribute damage from gas grenades?
Lone Wanderer: (Level 4, Wording) Does this apply if you're stealthed and the party can't see you that way?
Demolitions Expert: (Level 6, Mechanical) How is cooking off a grenade going to differ from just throwing it outside of how it's roleplayed? Typically, whenever a friend of mine uses a grenade, the GM just takes into account the AoE and says it hits so long as they get the roll. If they don't, it doesn't hit anyone, or on a crit fail, might hurt the player in question. My idea on how to fix it is to make it a preventative perk, either increasing the difficulty for an enemy to spot and disarm your explosive, making it less likely that you hit an ally in range of the blast, or granting the explosive in question a DT penetration, so long as it's a thrown or placed explosive on all matters. Explosive projectiles have range
Pathfinder: (Level 6, Subjective) I just don't see how this is useful at all to want to blow a perk on it. I've never been in a game in which getting anywhere on a map-and-compass scale 25% faster would've changed anything, nor have I been in a game that's ever used a sky bandit, which to me seems like a pretty narrow use since it only affects one kind of vehicle. My suggestion to correct this is to make it so that you can roll a survival or perception check whenever a GM would roll up a random encounter to see if you can avoid the random encounter or at least avoid an ambush.
Ammo Crafter: (Level 6, Wording/Mechanical) I don't think there's any system in place for recovering ammo, nor would anyone really want to deal with it. So, I'd personally simply get rid of the first part altogether and make this what you need to make the "Craftable" ammo for firearms. Maybe make it a "Firearms" reliant thing instead of a Mechanics thing so that there's a reason to have firearms over Battle Saddles.
Vigilant Recycler: (Level 6, Mechanical) Outside of "Optimized" ammo in uSea's list, there aren't any craftable ammo kinds for M.E.W.'s, nor does anyone want to roll if they keep the hulls, casings, or batteries since it's really too much trouble for too little pay-off, and I don't think there's a system in place even if they wanted to recycle. So, let's just make it the equivalent of Ammo Crafter, throw in the optimized stuff, and maybe something else. Armor Piercing or Silent Ammo, anypony?
Organizer: (Level 8, Subjective) There's nothing really wrong with this, but, well. Carry weight in Fo:E is a joke and that's the way we like it. I just don't see the point in having it being something to worry about since you're co-operating with five other ponies to shoulder the weight with, so I don't see the point in stuff like this perk.
Super Slam: (Level 8, Subjective/Wording) Doesn't seem very "Super Slam"-my based on the effects written. I get why it is, but maybe we could rename the perk "Will Knock You Down" or something.
Sharpshooter: (Level 9, Wording) Since perception has no influence on what your range is for your weapon, I believe, the second perk is the only useful bit there.
And Stay Back!: (Level 10, Mechanical) Okay! This is actually what I started this big, stupid list to mention! Since pellets are no longer a thing we have to worry about (at least in uSea's weapon list, I think it still works fine in Ten's as long as you use the damage rolls to determine knockback), this has lost all meaning! So, how can we fix it? Well, I talked it out with uSea, and we came to three possibilities!
One: Make it a flat amount of push movement per turn on a hit target, resistible on a strength check.
Two: Simply use the damage on the d10 rolls to determine if you move 'em. If you roll a ten, you move 'em a set amount. Multiple tens push more.
Three: Have it push a hit target for as many units as the damage done to it divided by 20, 15, or 10 at Medium, Short, and PB respectively.
I like option three the best, uSea's split between two and three, but it's really open for discussion.
How We Do It On The Farm: (Level 10, Wording) Do we take the multiplier for a critical, 200% for example, and then add 50% to the multiplier itself, or do we add 150% of the total damage done on a critical hit on top of that critical hit? Or does it make a difference? My head's kind of buzzing right now.
Chemist: (Level 14, Subjective) How long do chems usually last? Is there a chart for it, or do we just kind of imagine it? I'd prefer it that if we didn't, we make one.
[Edit: We actually totally do! It's in the Misc. Items section!]
Celestia Powered: (Level 20, Subjective/Wording/Mechanical) You know, since we do have some games that take place before and after the cloud ceiling, we really should write something down here.
Amanuensis: (Level 22, Mechanical) Why is this even here? I've never run into a blank magazine in my gaming experience, nor at this point would it even be useful. Either lower the level requirements, or just remove it altogether. Judging by what Kkat herself said, I'm leaning towards the latter.
Don't Touch That!: (EP, Level 2, Subjective, Mechanical) First off, I don't think there's an IED underneath Ten's or uSea's list for you to make. Second off, if ammo for firearms and M.E.W.'s can be crafted by everypony, why is ammo for... Well, why are thrown explosives so special? Either make 'em all EP things, or make 'em all general.
Also, someone's been playing too much "Doom" if when they think of 5mm ammo, they think of a chaingun instead of Assault Rifles and Miniguns.
Raise That Barn: (EP, Level 3, Subjective) I've never seen this picked or used because, for the most part, in a six pony group, only one or two of them are EP's. Maybe just make it so that if they're working on a project with anypony else, they're making it go 25% faster per EP with the perk.
Strong Back: (EP, Level 8, Subjective) I still think this is funny.
Bombermare/buck: (EP, Level 9, Subjective) Can somebody please explain to me why this is an EP exclusive other than "Well, we had to give them /something/." Because I think that's a lousy reason to not give something that'll be useful for every explosives expert to everyone.
Bonsai: (Ghoul, Level 12, Subjective/Mechanical) Why is this even a thing? If anything, it should simply be a quest perk or something.
Contract Killer/Lawgiver: (Griffons, Level 2 [General, Level 14], Subjective) I've never seen anyone pick up this perk, nor do I see it being useful in a day-to-day basis. Maybe if it gave a damage or to-hit bonus on folks that have a bounty on them, it would be considered a more "useful" perk to nab up.
Broad Daylight: (SATS, Level 26, Subjective) Are you friggin' kidding me? I get that Pipbucks can cast "Light" like the general Unicorn ability, but for a level 26 ability to not get noticed while casting it, I would expect that it could also shoot infrared laser beams. Or miniature sharks.
Matrix Casting: (Unicorn/Alicorn, Level (2?), Mechanical) You know, it never really goes into detail of what matrix spell casting actually does to the spell. Does it combine the potency of both unicorns/alicorns? Is versatility a factor?
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Oh, wow. I started doing this list at around noon. It's 11PM now. Forgive me for any opinions that are a little half-baked, and I welcome any criticism to how these perks work or if they're viable or... Well, if my writing style makes you want to pitch baseballs at my handle. Anything, really.