Okay, I got it: if there's widespread literacy, why isn't there widespread democracy?
Eh, I've been to a few places with a lot of one and very little of the other, I don't really see these two concepts as having all that much correlation. YMMV, of course. A decent in-game explanation? Traditionally having a productive, comfortable middle class is among the strongest factors prompting democracy, and many of the nations of Khorvaire don't really have that. Plus, the patriotism/nationalism/jingoism of the Last War could really put a damper on pushes for government reform - and as long as people are concerned that the next spark could kick off renewed fighting, widespread war is politically and militarily inconvenient, with those who clamor loudest for reform being labelled as enemies of the state. This question is really hard to answer with one single generalization, I guess it really depends on individual societies.
And why the heck are the Dragonmark houses the only ones with the monopolies? I mean, in theory anyone could be making money off magic item creation, or messages, or trains.
The way I see it, their advantage is that 1) they have a leg up with inherent inherited abilities (dragonmarks) that naturally lend themselves to particular industries, which helped make the houses competitive; and 2) they were just there first (that is, the first monopolies, not necessarily the first companies into any particular market). The dragonmarked houses had an advantage in an open market of having renewable magical resources that didn't require training or years of study, just an accident of birth. After that, they had the advantage of forming their companies around a family unit, which helped them keep the company together and keep everyone focused on the good of the company.
The dragonmarked houses also have the advantage of market momentum keeping them in place. They have offices all over the place, incalculable wealth, and centuries of history behind them. That kind of power is hard for anyone to compete against. People do compete with them though, but by and large their options are 1) let the house buy them out, the way corporations in our world do with successful startups; of 2) get crushed by the full might of the Twelve. There's a reason that monopolies in the U.S. existed, and why they had to be dismantled by government action. Once a corporation gets a monopoly, they become able to turn market forces to their own benefit to maintain that position.
Why are gnomes in charge of messages, while elves are in charge of illusions/shadow? I mean, gnomes are the illuionists, traditionally. Or inventors, and Cannith got that.
I think this one just comes down to averting stereotypes in order to make the setting unique. The only reason those things are expected of certain races is that they were done that way in other settings. One might ask similar questions of racial treatments in Dark Sun, for example, and likely get the same answer.
Why are there evil clerics in good religions when there's a plethora of low-level detect alignment spells? (ooh, that's a good one) Especially since the Silver Flame is all about rooting out evil? What, they're unaware of the idea of alignment when they have spells for this stuff?
This one bugs the hell out of me, and is a huge inconsistency. How does a church with hundreds of paladins have evil priests that go unsmited? While there are ways to go about hiding an evil alignment, it's hard to argue that a low-level cleric or lay priest has the means to keep their nature concealed for any significant period of time from a paladin. The Silver Flame even has an Inquisition specifically to root these guys out. Maybe there's just so much selfish, looking-out-for-number-one evil around that smiting everyone who pings your evildar is unworkable.
I simply handle this one by cutting
detect chaos/evil/good.law out of my game entirely, and giving paladins
detect undead instead. In a world like Eberron, I dislike the idea of being able to spot evildoers at will, it detracts from the pulp/noir portion of the setting for me. Again, YMMV.