Just about anything would be better, although while usually technically still viable, warts n all - it’s not the point. It’s like getting in a 600HP sports car that has a big sign on the dash saying: -20 Horsepower +10% motorcycle handling. While not that impactful, It’s still an insult to injury and most likely piss you off.
Most frustrating part is definitely a “perk” having a draw back. Literally doesn’t make sense. So the thrall levels up and now its worse? No sense, get rid of the -att nonsense.
I’ve explained that before, even had another player once write that perks are perks (whether good or bad…) 
If you Google search the term you’ll get an example from the game: Kingdom Come: Deliverance who use it as well.
Either lack of basic education or adaptation from other games I suppose.
That should be called an adaptation or alteration, not a perk.
“We’ve added a new perk to your job based on your continued, and valued performance. The perk? You can can keep an extra picture on your desk, AND we’re gonna dock your pay a couple thousand dollars a year.” That sentence does not make sense.
Neither does the bit about bowmen “losing bulk”. I get that it’s both a balance concern and a trope (agile, elf-like bowmen etc) but in reality firing a bow requires serious muscle.
I would like to see something like that.
And what happens to all these bad perked thralls? Players spent time leveling them, dont want that time to be a total waste, so they end up on guard duty at a base…more thrall lag…less bad perked thralls, less thrall lag…
Most people I know either delete or childishly rename them to release steam. Ones that I had, I placed somewhere where there was a dire shortage until I got better uns, then deleted them.
My Aesir and J’sag warriors all have a particular tag atm. 
but that’s due to combo failure.
If I am on a pvp server, build a theme castle and put them in it and ask people to raid it.
Break bond on rubbish perk thralls. Sacrifice the unworthy to your god of choice. Sure, you can’t harvest the bodies, but it’ll make you feel better when you get a woeful 'zerker with 45% str chance that insists on learning archery perks… or that rare 100% str chance 'zerker that dumps all their points into accuracy, then grabs a bunch of str reducing perks.
I still dont mind the negaperks. The thrall wants to be special, so let it be special. And besides, most of a thralls hitting power is innate and behind the curtain, so whether the st stat that shows is a 59 or a 29, that hidden .8x damage multiplier means they both suck.
They need a better way to deal with thrall perks. Maybe a Thrall Perk Scramble Potion…?
Or a way to selectively breed the perks you want. Maybe sacrifices to the Gods could earn potions that would grant thralls perks based on which God you got the potion from?
That could work, but the main issue as I see it is that FunCom has labeled the thralls, made that label mean something in the back-end system, then introduced a front-end system that messes everything up.
Fighters starting with high accuracy.
Archers starting with high strength.
Both frequently not only gaining their off attribute faster, but earning bonuses to the off attribute and penalties to the main attribute.
I wonder if this would have been more acceptable if the tag or title (and associated back end bonus) reflected the thrall’s current attributes, adjusted at each perk level (0, 10, 15, and 20). Whichever attribute is the highest at those levels determines the thrall’s title.
Strength = ‘Fighter’ = melee bonus/damage bonus
Agility = ‘Acrobat’ = armor bonus
Vitality = ‘Meat Shield’ = heal rate bonus
Accuracy = ‘Archer’ = ranged bonus/to-hit bonus
Survival = ‘Survivor’ = reduce debuff + ‘I ain’t dead yet!*’
- ‘I ain’t dead yet!’ = rescue/recover dead thrall with cost of permanent loss of 20 survival. If survival drops below another attribute, thrall loses the ‘Survivor’ title and assumes a new role.
——
So, a thrall could start out as a ‘Archer’, only to change to a ‘Fighter’ once levels and perks invariably change the attributes around. Almost all Darfari would be ‘Survivors’ unless rescued often enough. And so on. overall complex and not likely to happen.
Actually, if they did it like this, then “Bearer” minions might be determined by Encumbrance, which currently isn’t a stat on Thralls.
They could also add Grit back in, and make it increase a thralls attack rate or aggro range. Sentinel might be good for these traits.
I think Hulk, Tank, or Guard might be what they would call a “Meat Shield”?
After all, it’s kinda odd for the thralls to be SAVAS instead of SAVAGES.
Of course, they never made a stat system for pets… ANIMALS would work well. Pets don’t really need accuracy the same way a thrall might.
Key- (reflected trait for context) [Pet Class]
A - Agility [Glass]
N - Natural Growth (Encumbrance) *this could have an effect on the SIZE of the pet. [Pack Animal]
I - Intensity (Grit) [Shepard]
M - Might (Strength) [Warbeast]
A - Awareness (Instead of accuracy) [Hunter]
L - Lifeforce (Vitality) [Escort]
S- Survival [Feral]
What I think happened was that they were short on time when they implemented the thrall stats and leveling, and the numbers they assigned to different thralls ended up being along the lines of “Screw it, this is the best I can do with the time I have, we’ll keep improving this as we go.” 
As for the rest of your post, let me say this first: I like it, I really do. But…
I’ve spent an unholy amount of time on these forums, and I’ve both read and written my own share of big, detailed proposals that would either introduce an intricate new system or basically rework an existing one. I won’t say those are useless, because they aren’t. But their main use is to generate discussion. They never get implemented. That’s why I try to make my suggestions as limited in scope and as incremental as possible.
Again, this is not a criticism of your idea, but rather an explanation of why mine was the way it was. It might look like a band-aid and it might not be what we would all want, but I’m kinda hoping that if I repeat it often enough, someone at Funcom might say “Screw it, this isn’t the worst thing we could do and it fits into this sprint.” 
With thrall limits these deadeye folks are all going to get deleted.
If there is no way to alter the rng on the named thralls (there must be), then maybe they could drop an experience boosting sigil for the next thrall we are training up.
I think I’m probably going to have to point out something that most players aren’t going to like in that the developers don’t think there are bad stats. There is nothing inherently wrong (in their eyes) with your berserker getting some accuracy, because someone might decide to put a bow on them or they might do what I’ve been looking at and giving them throwing axes and javelins.
I’m not sure they are even going to agree that Perks that have a bonus and a negative are necessarily totally wrong either.
It seems evident and logical to players, but they aren’t only players.
I might have agreed with that before finding out about hidden damage multipliers. I forget whether it was Firespark or Wak that first explained those in a video, but you can find it on YouTube. Long story short, every thrall archetype has a damage multiplier that you can’t see anywhere in the game UI.
Oh, also, fighters get a penalty on ranged damage and archers get a penalty on melee damage. Or at least, that’s how that used to be.
All in all, I can’t think of a good non-RP reason to give your fighter a bow or your archer a melee weapon.
If Funcom’s stance is “there are no bad stats”, then they really should make the in-game math reflect that stance
Do they get no benefit from ranged accuracy damage for melee at all? Or do they get a smaller benefit?
Because that’s a pretty important distinction. Just because it’s not super-optimal does not make it a bad stat increase. It’s just not the best or min-maxxed one.
And I’m pretty sure devs hate people only min-maxxing.
DISCLAIMER: I haven’t run the numbers in ages, so I don’t know if the situation is different now. I can only talk about how it used to be the last time I bothered to check.
Basically, if you don’t pick the correct archetype, the bonuses from the stats don’t matter. And that applies to both fighters and archers. So, if the current best fighter in terms of hidden damage multiplier is (for example) Dalinsia Snowhunter, then it doesn’t matter what strength bonus you get on your Lian, he’ll never be as good as an unlevelled Dalinsia.
Which is why I was implying that nobody would put a bow in a fighter’s hands, because it would never compar to a decent (not even the best, but just decent) archer.
But again, that’s the way things used to be. I stopped obsessing over stats because I don’t play PVP where they matter much more. Yes, it pіsses me off to no end to get a Deadeye perk on a fighter, but it’s an objection on principle – “I spent hours leveling this thrall and you do this to me?!” – rather than something essential for my character’s survival.