1a) Does it not say "damaged by collateral damage"? All siege units have a collateral damage limit, after which they cannot do any additional damage (you might have noticed that they become unable to attack in such a situation). With this change, city defenses also provide an intrinsic collateral damage limit. 100% city defense protects against all collateral damage, with 80% city defense unit can only be damaged to 80% etc. The idea is to favour defense bombardment over an immediate outright attack using siege weapons which was too powerful before.
1b) Public Welfare and the Thai UP provide extra commerce per excess happiness, Totalitarianism provides extra production per unhappy citizen. Both of these are capped by city size, i.e. even if your excess happiness is higher than your city population you cannot get more commerce from that.
2) The idea is better horse breeding and greek fire etc. respectively.
5) Sure, but that is often the case with URV goals.
7) Yeah, but the tech tree is also more regular and predictable now, and more content has been added to make every (admittedly most) techs meaningful. Part of the original motivation to do this came from my feeling that DoC had added too much for the basic tech tree, leading to overburdened techs. I guess its a matter of taste. The rigidity of the tech tree necessitated the addition of some techs that I otherwise would not have included just to have reasonable connections between all of them (dig up the old discussion thread if you want a taste of the hand wringing I did), but I'm pretty happy with how it turned out and which techs ended up being included. For example, Bloomery is code for Iron Working, which is a singularly important technology. Likewise Leverage represents all forms of classical
simple machines, like levers, pulleys and the wheel. I decided to use this more general idea (as opposed to The Wheel) for better connectivity to other techs and keep the tech plausible for civs that did not use wheels (i.e. Amerindian civs).
