So I've been wondering about these sims and those traits and why is it that they often have so many friends? The mean spirited and evil traits state that those sims prefer to have enemies, yet when left to their own devices they often end up with lots of positive relationships with other sims and still interact in good ways etc. I find this troubling.
I decided to play one of my newest town's evil sims. He is Abbadon, and I created him to be the town bully and all-around bad guy. He is Evil, Inappropriate, Mean Spirited, Genius and Animal Lover (I wanted him to at least like his pets, he has a dog and cat and the Genius is so he'd be a good criminal)  When I finally played his character I found he had positive relationships with half the town. Good sims, Friendly sims, Brave sims etc. Including the 4 houses/families that I play in this town!  All of them must have been forged when I was not playing those families though. None work with him because he's the only resident who's in the criminal career other than one townie who I left as the criminal boss but never play.   
I also tested some theories based on the info I got from people here about sims and infidelity!  Yet this sim VERY easily split up 4 completely committed couples with no trouble at all. Those sim couples had absolutely NO other flirts, all had the faithful moodlets, all had some type of family oriented or nurturing type of trait. All had kids, etc. And because he had a good relationship with those sims,all I had him do was use the Romantic interaction of "heat of the moment kiss' and poof!... every sim went for him with little or no effort.  He even seduced a straight and married male sim and his wife in the same park within an hour of each other. This is the flaw in the game mechanics that I really hate.
Why wont sims stay angry with them?  Who slaps someone, fights them and two seconds later talks about art or cheers about shared traits? It's so annoying! It's bad enough that in the middle of fights they will congratulate each other if they have a shared trait, but I'd rather most of my sims avoid and keep those sims as enemies. 

Can I create a caste system that will keep evil and bad sims from having friendships with sims with certain traits? I mean, I doubt the game would have had Abbadon go after sims the way I had him do, (and I did not save that game btw) but the fact I could break all my main sim couples up so easily with one click really bugs me. I get that there will always be a few people, even IRL, who are oblivious to horrible people and even befriend them and since I try to play realistically I'm fine with a few sims having friendships with my evil sims, but I wish the other sims would dislike them and stay that way! Especially my main family. What I am going to do for now is be sure my 4 households I play do not like this sim, and maybe with some proper suggestions and mod-tweaks I can get things the way I'd prefer?

I can't help you with the your caste questions, but I do agree that there are inconsistencies in the trait system such as you note. Also Loner sims, for example, role the wish to make friends with someone far too often in my opinion. The game can also generate Sims with both the Mean-spirited and Friendly trait, too, which I find annoying. I believe this is inherent in the game's basic programming, perhaps in relation to the "Social" need? I can't remember if mean interactions fill this need for a mean-spirited Sim or not?

I'm kind of at a loss as to what to suggest here myself, this should be an interesting conversation as more contribute to it. But just wanted to point out that Evil in particular does not mean anti-social. Evil sims delight in the misfortune of others and the trait is the opposite of Good, it doesn't conflict with Friendly. My Evil sims have lots of friends. When I play them myself, they tend to seek out other Evil sims to hang around with. My Mean Spirited and Grumpy sims may try to have lots of friends, but can (although not always) have more difficulties in actually keeping them.

I suppose I'd like it better if those "bad" traits were a little more realistic. I do get that evil sims can have many friends, in fact the worst kind of people can often be quite charming. I'm sure most of us have heard about serial killers who often were pillars of their communities and people were often shocked to know they were murders. But basically I'd like things to play out to where if someone really dislikes a sim, they don't run up to them and excitedly talk about weather or gardening. LOL

And especially I'd rather faithful sims were not so easily swayed just because the liking gate is high between two sims. That's why I'd love them to create a no-nonsense FAITHFUL trait to where a sim would flat out refuse any sim who hit on them. Like the way they do if  the sim is an acquaintance. But you get that liking gate over 60% and it doesn't matter what kind of sim you have, they will smooch and make-out like it was nothing.
-- Not for nothing, but it would kinda be nice if that was more like real life. LOL --- I'm kidding.