THREE TINY ESSAYS ... IN POINT FORMAT. I am lazy and have a lab to do later, okay. A great deal of this is speculation and headcanon, which means I will modify it the second canon gives me anything concrete.
Spoilers throughout.
A) The Rise and Decline of the New Human Empire
* the Empire probably didn't start out with Seth as the uncontested head--she might have been the only Nightlord commander left, but it didn't mean she was fit to govern all Methuselah all on her lonesome. She probably had a council thing going, and was inexperienced as hell the first few decades, which is why at grass-roots level the system is kinda off.
* Methuselah history says the Empress led them to a barren new land and made it green again, and safe for them. The second part is true--the Empire has/had access to super-advanced technology from the Armageddon. The first is not; they were essentially banished by Lilith's forces, and had lost cohesion and a solid power base, because two of their commanders had vanished.
* The Empress became veiled early, and perhaps set up her doubles system early too; by the time the first loyal generation of Methuselah died, everything about Seth's origins had become secret from her people. This was probably around the time the noble hierarchies were established.
* Seth came into actual power and mental maturity (without requiring advisers) too late--the Methuselah customs and biases had by that time been too deeply ingrained, and she could not create the sweeping social and thought reforms needed to create a view towards coexistence Empire-wide.
* Relating to the previous point--Seth probably didn't even desire coexistence for a long while! She was bitter, she was just as prejudiced as Cain and Abel had been, she shared this viewpoint with the great majority of her subjects. The Seth we see in canon is one hell of a mature character at base, but she didn't necessarily reach that as fast as she should have to be truly effective as a ruler. By the time she was okay with sharing the world with Terran, her Empire wasn't. At all. If it ever was.
* She eventually got caught between a rock and a hard place--she couldn't rule well but it was better for her to be ruling than for there to be anarchy. That started crumbling as successive generations lost faith in a faceless Empress, who could really be anyone. Suleyman definitely couldn't have been the first of his kind--he was just the one she destroyed her secret for. It was probably going on for oh, two or three hundred years before most of the TB protagonists were even born. Faith like Astharoshe's or Ion's (the Empress's ways are mysterious but I believe in her) is not common. The nobles don't really believe in the idea of the all-knowing Great Mother, they're just used to having her as the leader and are comfortable with the status quo.
* Crusnik 03--or just Seth herself--killed/assasinated/discredited/WHATEVER THE HELL IT TOOK to covertly crush revolutions and eliminate dissidents. I like to think this is the majority of the people she had to kill over the course of her reign, but that's not likely.
* Esther is correct when she says the Empire's coexistence is flawed because the Empress still holds Methuselah superior to Terrans. Terrans are treated well in the Empire, yes, but they remain 'property of the Empress' and mainly serve the Methuselah. The Methuselah, meanwhile, are Seth's 'children.' GUESS WHICH ONE SHE OBVIOUSLY PREFERS.
* Seth also deals with Methuselah (particularly nobles) much less harshly than she should. Take Endre Kourza, the Methuselah who murdered another noble and a shitload of Terrans. He was regarded as a 'monster' by the majority of the Empire, especially Astheroshe, but Seth didn't kill him, as she might have been expected to. Instead, he only faced exile--and thus was free to kill even more Terrans--and the Empire only took responsibility for him when he became a concern to the Vatican and war became a visible threat. I think that would have pushed him to execution in the Empire at last, but Isaak got to him first. 8(
B) Seth's Mother Issues
* YEAH YOU READ THAT HEADER RIGHT.
* Over the centuries Seth recreates herself in the image of the 'Great Mother'...this was probably an effort to replace Lilith, or emulate Lilith, as well as being counter to Lilith's Vatican-given title of 'Dark Saint.' It's Seth's acknowledgment/homage to her mother figure and an attempt to become a greater one, I guess.
* She probably didn't know she'd done it in those terms, not consciously, for awhile, but--Seth's had 900 years to evaluate everything she's done. She's aware now.
* ...she's aware of her 'inferiority' to Lilith, both in terms of motherhood and in terms of relations to Abel. This doesn't touch her relationship with Abel much since it's essentially a strained little thread, but it's there.
* However, she doesn't allow it to upset her anymore; she's accepted Lilith being the superior one in terms of being an important person to someone (namely Abel) and has learned to deal with it. It helped--really helped--that she loved Lilith too.
* Seth also has a kind of emotional disconnect now--it comes out differently around Abel but it applies to pretty much everyone she knows, although it doesn't show in conversation at all. She can care for people as a whole, she can care for individuals, but she can never become wholly, closely involved/devoted to anyone. This even has a visible manifestation in her actions: she takes on a ridiculous number of roles in her life, but she never is actually just one of them. The doctor's student is a detective, too; the tea-seller is the Empress; Seth the girl is also a killer.
C) Seth's Insanity
* So if there's one thing Trinity Blood teaches us, it's that wacky alien nanomachines do bad shit to you. Lilith ... we have no idea, because she ded now. Cain is batshit insane form merging 100% with his and taking Lilith's. Abel's soul contains nine centuries of PAIN AND HURT AND DESOLATE WASTELAND which makes him a little bit crazy at times. And by a little I mean a lot.
* Seth is not an exception to this rule. I still don't know the source that claims she allows Cain to kill her because she can feel herself going insane and she knows that means the Empire will fare better without her at the helm, but I'm taking it as a fair canon extrapolation and running with it.
* The Crusnik are little voices in the back of her head that tell her to eat Methuselah. The rational part of her genuinely considers the Methuselah her children. It's a hell of a tough battle, Seth doesn't have a guilt complex but she is guilty, all the same, when she has to give in to the Crusnik, and I'm not surprised if she's grown a bit unbalanced as a result. I mean, seriously, nine and a half centuries of that? Most other people would want to off themselves too.
* It's one hell of a sign how self-aware Seth has become, too, if she can literally feel herself going nuts.
* Humans aren't really mentally designed to live forever. Look how weird the Methuselah are, and they get three centuries and a bit, maximum.
* Seth hates the Crusnik nanomachines and figures history could have done way better without them. Her method of death--sacrifice herself, give Cain her nanomachines in the process, which isn't good for him and might give Abel an edge--is a way to, essentially, start removing them from the world. Which is selfish, if you think about it, because it hinges on Abel succeeding, and he'll end up carrying that particular cross alone.