Back when I was a Christian, the question that really troubled me and spurred my intensive study of theology was Why are there so many religions? Randal offered his interpretation of my question, which I think is pretty accurate:
He doesn't spend any time on the first, instead just linking to some other material. But the reason I found it a troubling question was to me fairly obvious: if God really desires everyone to be saved, then why not intervene in humanity long before we'd diverged across all the continents? Or why not reveal the One True Faith to everyone, instead of having a seemingly arbitrary "chosen people"? It struck me as revealing that only the Israelites, and no one else, referred to themselves as God's chosen people. From an anthropological perspective, that's hardly surprising.
The plurality of faiths has provided humanity with little more than conflict – often bloody. People were converted by the sword in Rome, the Inquisition, the Saxon Wars, and Encomienda (among others). Religious violence persists to this day as one of the most brutal, depraved and pointless sources of violence in all of human existence. Israel and Palestine can't reach peace terms because they're both convinced that God gave them a certain patch of land in the desert, and they're willing to murder and sacrifice themselves for it. Muslims are blowing people up and subjugating women while Christians in the third world burn witches. It's utterly fucking ridiculous.
This is a big deal because it didn't have to be like this. God could have simply revealed the truth equally to all people. It would have spared humanity an incalculable amount of needless violence and suffering. But for whatever reason, God supposedly decided to hone in on the people of the tribal Middle East: "That's the best place and time for me to reveal my One Truth Faith to all of humanity!" I don't think there's any convincing rationalization to get rid of this problem for Christianity. It makes Christianity look a lot like pretty much any other religion on Earth.
On the second question, Randal elaborated a bit:
Analogy fail. The obvious truth is that we don't know any absolute description of reality. I've talked often about model-dependent realism and I'm big on it. It eliminates the fuss about what's real or not (hear that, free will debate?) through the simple observation that our understanding of reality comes to us by way of descriptive models that are more or less successful to varying degrees. Our cognitive models are some of the most limited, and science often demonstrates this by revealing reality to be highly counter-intuitive.
This doesn't create any great existential dilemmas; it simply says that our best understanding of reality is contingent upon the evidence available to us. What I think Randal misses is that to really reach a more enlightened place (yes, I realize how cocky that sounds), you have to let go of your beliefs and assumptions. You can't hold any idea as sacred, and you have to treat them all with equally ruthless skepticism.
In my experience, Christians often switch very subtly between offense and defense. For example, William Lane Craig always posits his Kalam Cosmological Argument as a logically air-tight piece of evidence that ought to compel rational skeptics to believe in a creator. But when he's pressed on the justification for the underlying assumptions – like the argument's reliance on the "Neo-Lorentzian interpretation of Special Relativity", he switches to defense and says (in so many words) that a theist can be confident that there aren't any resounding defeaters for their position. In other words, the theistic arguments can't be disproved.
But that's missing the point. I'm not interested in hearing theists defend their assumptions after they've made them. I want to know how they got to those assumptions in the first place. But in order to do that, as a believer, you have to let go of your emotional attachment to sacred ideas and imagine yourself as a true-blue skeptic starting from scratch. And inevitably, when you press a theist on the evidence that ought to compel a rational skeptic to assume God exists, they'll switch from offense to defense – retreating to vague and esoteric philosophical arguments fussing over semantics, appealing to what's possible, and presuming victory over their interlocutors when their assumptions can't be conclusively disproved.
Randal stumbled when he lumped "skeptic" in with "Christian" and "Mormon". "Skeptic" should always be the default position – y'know, what is known in philosophy of science as the null hypothesis. If you make the assumption first and then look for "defeaters", you're always going to be able to conjure up some rationalization that prevents your assumption from being disproved (see for example the comments from Christians here). An honest self-critique requires that we divorce ourselves from our assumptions and challenge ourselves to get back to them. That subtle but pivotal shift in perspective is the difference between a career apologist and an ex-Christian.
p.s. – I just remembered that the mighty Bud Uzoras did a terrific post on this topic some time back, using the infamous Parsec Apologetic from Star Wars as an analogy. Check it out at his blog, Dead Logic.