The Bacillus nanomachines that grants the Methuselah their powers gives them practical immortality, super strength, speed, healing ability and magical powers. It's only drawbacks seem to be making one susceptible to sun damage and giving one the craving for human blood cells. Given the awesome powers this Cursed With Awesome power grants, why don't more people deliberately infect themselves with it? The sun thing is easily overcome with Applied Phlebotinum, and one assumes that, in the highly advanced future, ways can be developed to generate a supply of synthetic blood cells (or massive amounts of natural blood via cloning technology, if that's not possible.) Who wouldn't give up their humanity for eternal youth and the ability to jump effortlessly from church spire to church spire? (If all of the people on Earth were of the same race, there wouldn't be a massive Cold War going on either, so one has to wonder just why humanity hasn't jumped on the vampire bandwagon...)
You said it yourself. Vulnerability to sunlight (which means a lot to many people, many of whom may not be able to afford the Phlebotinum), and the blood hunger. Who do you feed on when everyone's a vampire? Not to mention the fact that effective cannibalism would squick the hell out of many people. Giving up one's humanity to become more is fine, unless you think the drawbacks outweigh the good.
The vulnerability to sunlight could be easily solved by those unable to afford the Phlebotinum by this nifty little invention called "roofs". And while it would suck to not be able to watch a sunset anymore, there are many people who would gladly trade that pleasure away for a shot at eternal life. As for the blood/cannibalism thing—granted, a means would need to be found for generating a large amount of synthetic blood to feed the population, and if that's not possible, cloning technology could be employed to produce large amounts of human blood cells. (And indeed, some scientists have already been able to do so on a small scale in this day and age. Just think what could be done in the future...)
Sunsets, sunrises, Daytime in general. Have you ever been stuck like that, not being able to go outside for hours at a time? It's maddening. Cabin Fever for half your life, forever and ever. Plus, other universes have even rougher restrictions, like running water being lethal(as in, you no longer have to fear a 9mm, but rivers, rainstorms, and even Super Soakers are now deadly to you). Or what about hunger? As you said, blood replication (assuming it works, a lot of supernatural stuff tends to have a "no technological shortcuts" clause) has only been done on a small scale. To feed a vampire nation, you have to be able to synthesize it like we grow corn. And be able to do it just as cheaply.
Oh, and let's not also forget the possibility that the Methuselahs aren't just handing out Vampirism to every Tom, Dick, and Nelly who asks. After all, the New Human Empire has to use a particle shield over the entire nation to protect their Vampire population in the daytime, which can't be cheap to make or maintain, and they need to keep a balance between themselves and Humans.
Yeah, the logistics of it would probably be a nightmare, and there would most likely have to be some means of population control implemented, but still, it's surprising that vampirism is thought of as such a horrible thing—its potential benefits for humanity even on a small scale aren't even explored.
Vampires have to be discriminated against so they can angst. They actually live off of angst. the blood drinking is just to generate more angst. Accept them and they would quickly die.
Except that the Methusulah generally don't angst. In fact the majority of them seem to have a superiority complex (they call themselves 'the true human race' for crying out loud). The nearest thing to angsting you get is with some of the Ghetto's inhabitants and even then it's more of a case of either weary acceptance or being justifiably pissed off. Regarding humanity's failure to jump on the vampire bandwagon, one of the things that goes unmentioned in the anime is that infection with the Bactillus doesn't always result in that person getting vampified. There's an equally large possibility of it either doing nothing and going dormant, or it killing the infectee. Add in several centuries of both sides hating each others guts and a heavy dose of human nature and you have your answer.
Woah, WOAH! Hold on. You're getting the Methuselah wrong. They aren't immortal, their life expectancy (300 years) is higher than Terrans (about 80 years? as ours). But they all die. Second, silver poisons them easily too, it cancels out any regeneration they have. Sunlight (UV Light) makes their bacillus overwork and eat their organs and own bloodcells in FIVE MINUTES. Their dome does allow them to filter out the sunlight, but they don't get real "sun" per se, Shahrazad envies Terrans and wishes to be one because she mourns losing the beautiful sunshine. But she's THE exception among Methuselahs, even Esther notes this. Also, the Awakening. You never know when your Bacilli will awaken. Sure, some people get lucky and they awake at their 20s or 30s, but imagine to live centuries as a 80 years old (some dudes of the Court are very old) or a 13 (Ion or Mirka) or a 6 years old (Endre)? Their infertility rates is so high they barely can reproduce, furthermore the Empire has retarded rules against Terran/Methuselah unions which would improve their fertility (if Mother is Methuselah, child is Methuselah). You can't control that. Not all get "magical powers", most of their abilities come from Lost Technology they wield (Astaroth's spear, Shahrazad's gloves, Süleyman's ring), most Methuselahs from special subraces (Radu, Kasper, Balthasar, etc. Except for Virginia Walsh) are all Orden, made to be antagonists. They are like the mutants/witches of the Terran equivalent (who also got speshful powers). They got it easier now, but centuries ago? When they arrived to Earth from Mars? When the Thirst took over them and turned many insane in Thirst, unable to defend themselves against UV or Silver? It was pretty shitty for them. There are huge drawbacks of being a Methuselah as there are huge ones of being a Terran.
Crusniks/Krusniks are the ones that can, theoretically, live forever. Their nanomachines/bacilli are better, but only the special test tube babies were able to survive being injected with this particular strain. We do not know what the percentage of Terran-born humans who become infected with the Methesulah strain is, but there's a strong possiblity that for some people, even the Methesulah strain is ineffective or fatal. In fact, I was under the impression that this was the reason that Methesulah/Terran relationships are forbidden in the Empire. Methesulah probably tried to turn their loved ones, and the resulting deaths led to the ban.
Considering that the primary protection for Terrans from Methesulah who want to prey on them is the Vatican, there is also the not entirely insignificant possiblity that people are afraid becoming a vampire will result in ETERNAL DAMNATION. Do not underestimate the power of religion. Getting 300 years instead of 80 stops being fun when those 300 years are followed by endless suffering as punishment.
Also? Not everyone WANTS to live forever. Really.
I'd also like to add that the bacillus are not nanomachines, but a type of hyper-advanced bacteria created by the Crusnik nanomachines, as stated in the original novels and manga.
The ending bugs me. Why was there such a hasty wrap-up of the plot threads?
Easy answer: It got cancelled. It may not be true, but it feels that way.
The correct answer: Author died mid-series.
In the anime Abel's promise not to kill anyone seems oddly flexible. It supposedly prevents him from kill Von Kamfer to save thousands of lives yet we see him directly killing Vampires and the promise does not seem to particularly exclude them. Why is this?
Except when does he kill vampires? The methuselah that he cuts in half in the first episode could theoretically survive his injuries if his two halves were put back together. The only other methuselah that he kills are the Death Hunters which were already dead to begin with. And for his "killing" of Enderle Kourza, it is only stated that Enderle did not survive his injuries in the English dub of the anime, which was more or less a mistake on the dubbing team's part.
He does kill Alfred of Mienz in the first episode, by crushing his heart; while a methuselah can survive being cut in half if their two halves are put back together, nothing can prevent death if essential organs (read: the heart or brain) sustain critical damage. This is actually why Deitrich enjoys sending out Death Hunters rather than coming up with more subtle means; to a puppetmaster like him, warriors who had their life, conscious humanity, and sense of survival all entirely lobotomized away will be more valuable because they can't think for themselves and make decisions that would at least keep themselves intact, meaning they'll never even question their simple orders like attack when they're being cut into ribbons.
Watch that scene more closely. Alfred rips into his chest and crushes his own heart. It's also stated as so in the first Rage Against the Moons novel. Alfred mentions something about "pre-hypnotism" in the novel, so it's likely that the Orden hypnotized him before the mission to kill himself if he were to reveal his backers.
Deitrich manages to provoke Ion's blood thirst by slicing into his jugular vein/shooting him with a special bullet. Either Esther or Ion could easily have died without Abel's timely help. Couldn't Deitrich have just researched a way to do something similar to Abelhimself while he was traveling with Astha, to at least stall for enough time for either Esther or Ion to die in the jail cell? Y'know, instead of just throwing a crowd of easily defeated Death Hunters at them? Would have also saved him the precious few minutes he would have needed to activate... whatever the hell that weapon was Abel didn't want him touching later on.