It is my understanding the the Big Bad's motives is to control civilization through controlling libraries; hasn't he ever heard of television?
One of the big bad's minions in the OVA can control TV and radio globally on every channel. I think they have TV pretty taken care of.
Toward the end of the series, around episode 25, when Yomiko breaks in to kill Mr. Joker and then just surrenders doesn't really make a lot of sense to me, since they did not have anyone she cared about that they could use as a hostage so she really had no reason to surrender, given her powers she could have probably easily defended herself and fulfilled her part of the mission.
Actually, it's because Yomiko being especially Technical Pacifist in the TV series. She doesn't "breaks in to kill", she does it to somehow convince Joker to stop his plan to The End of the World as We Know It, without a single person dropping dead. And it ended exactly that way.
How many crippling, flashback-laden emotional deficiencies can one person HAVE, anyway? Is it just me, or do the villains du jour just seem to be making shit up about Yomiko's past to make her all depressed and mopey as a gambit for distracting her? Seriously. Read the manga, then watch the OVA, then watch the TV series and notice that this is what takes Yomiko out of EVERY FIGHT. She's said to be the most powerful paper user on the face of the Earth, she single handedly destroyed the British Library, can do anything she bloody well pleases with paper including blocking bullets, slicing buildings in half, and generally shred anything or anyone to smithereens. Why does she just open that stupid can of whoopass and be done with it?
She got all that power by being an introverted bookworm. She hasn't practiced her people skills enough to defend against a bit of psychology. Plus, her life has been manipulated at least a teensy bit in the past. Some of those tragedies were probably set up intentionally. (At least one of them was...)
The manga is a little more reserved in the application of her powers, but the animated adaptations basically paint her as a smalltime god who's too mushy to be properly effective. In the anime was powerful enough to destroy the entire British Library in one shot. You're telling me she couldn't just convert Joker's men to chum, paper-mache Joker's puny ass to a lamp post somewhere, and just slice the important bits of his base and machinery to ribbons?
One can argue that reading that much will obviously will make anyone Dangerously Genre Savvy. And after that, you'll be afraid of violence like hell, just because violence eventually turns you into Big Bad. On another note, never unleash violence against Magnificent Bastard, or you'll end up being named "horribly evil" to the rest of the world, while the bad guys will prodly stand under "saintly good" banner.
She used to be one of "Joker's people". There's a difference between mowing down hordes of mooks and killing the folks who shared a toast with you at the last New Year's party.
Perhaps I'm aiming for an unrealistic level of realism here, but how come Anita can do all those spectacular moves, but we never see her training or exercising?
It bugs me that, with the possible exception of Beethoven, none of the Ijin cloned are very important historical figures. Lilienthal's gliders didn't lead to a revolution in travel and at best all he did was help set the stage for the Wright brothers. Wilcox invented basically one thing, and Gennai's elekiter was derived from an invention from the Netherlands. Genzo Sanjo and Ikkyu are well-known monks who influenced their cultures and have many stories written about them, but they didn't really do anything. Fabre did a lot of research, but didn't really create any theories (Darwin did that). It's entirely possible that Mata Hari was never a double-agent, but just a scapegoat for France. Either way, she was caught and executed too fast to be considered to be a very good spy for either side. (And she probably couldn't phase through objects either.) Even Beethoven is simply known as a brilliant and influential music composer. None of these people (again, with the possible exception of Beethoven) really revolutionized anything.
In fact, let's replace all of them with more relevant figures:
Lilienthal gets replaced by Wilbur Wright.
Gennai gets replaced with Nikola Tesla.
Wilcox gets replaced with Henry Ford.
Beethoven can stay, because at least he's considered the most influential composer who lived.
Genzo Sanjo can stay too, because he's more based on his fictional exploits anyway.
Ikkyu gets replaced by Rasputin, who at least wielded some political power and has a reputation for being sinister.
Fabre gets replaced by Charles Darwin.
Mata Hari gets replaced by Richard Sorge, who is considered one of the most important and successful spies of all time. (Make him a gender-switched version if you want.)
I wondered about this as well. I imagine that it was because the writers didn't want to look lazy when and use notable figures that people could name off the top of their head. I know this sounds funny, but Japan has tons of Historical Domain Characters that would make you roll your eyes if you've seen how many times they've been used (Aleistar Crowley, or St. Germain for example). Your Ijin list is impressive nonetheless.
Why did the British Library think that resurrecting Gentleman would bring about a better world when anyone with a basic understanding of history (Which a secret organization made of librarians should have) would know that he didn't do a very good job of that the first time around?
The opening of this trope's summary has [Yomiko's] power results in an insatiable addiction to reading that rivals drugs. Yomiko literally must spend thousands of dollars a week on reading (just in case you did not figure that out from the title). Having watched the OVA, and briefly read about the other series, I cannot find anything about this. I admit that it would make sense (from the title) and would explain Yomiko's bibliophilia, but I cannot find any source that backs this up. And I'm still scratching my head at this "rival's(?) drugs" thing.