The article on theistic modal realism is ingenious. (One-sentence summary: God's options when creating should be thought of as ensembles of worlds, and most likely he'd create every world that's worth creating, so the mere fact that ours is far from optimal isn't strong evidence that it didn't arise by divine creation.)
I don't find the TMR hypothesis terribly plausible in itself -- my own intuitions about what a supremely good and powerful being would do don't match Kraay's -- but of course a proponent of TMR could always just reject my intuitions as I'd reject theirs.
However, I think the TMR hypothesis should be strongly rejected on empirical grounds.
It is notable -- and this is one element of a typical instance of the Argument From Evil -- that our world appears to be governed by a bunch of very strict laws, which it obeys with great precision in ways that make substantial divine intervention almost impossible. It seems that there are many many many more possible worlds in which this property fails than in which it holds, simply because the more scope there is for intervention the more ways there are for things to happen. Therefore, unless the sort of lawlikeness we observe is so extraordinarily valuable that tiny changes in it make a world far less likely to be worth creating, we should expect that "most" worlds in the TMR ensemble would be much less lawlike than ours: e.g., we might expect prayers to be commonly answered in clearly detectable ways. So how come we're in such an atypical world?
Generalizing: I think we should expect that for most measures of goodness X, worlds with higher values of X should be dramatically more numerous in the TMR ensemble unless increasing X reduces the number/measure of possible worlds much more drastically than for most other choices of X. (Because when you increase X, you get the chance to reduce Y or Z or ... a bit. More choices.) Therefore, we should expect that for measures of goodness X where "better" doesn't imply "much more constrained" most worlds (hence, in particular, ours, with high probability) should have values of X that are close to optimal, or at least far from marginally acceptable. This doesn't seem to be true.
It seems to me that counter-arguments to these are likely to be basically the same as counter-arguments to the original argument from evil.
The other thing about TMR is that it undermines any version of theism that expects God to behave as if he cares about us. If TMR is right then, any time God has the option of doing something to make your life better, then he forks the universe vastly many ways and tries out every possible option (including lots of ways of doing nothing, and even ways of deliberately making things worse for you) apart from ones that make the whole universe not worth while. As mentioned above, it seems to me that this should make us expect that visible divine intervention should be pretty common, but in any case it's not terribly inspiring. A bit like having a "friend" who, any time she interacts with you, rolls dice and chooses a random way of behaving subject only to the constraint that it doesn't cause the extinction of all human life. Similarly, you've got no reason to trust any alleged divine revelation unless its wrongness would be so awful as to make the world not worth creating. (These arguments are again closely parallel to ones that come up with the ordinary argument from evil, in response to responses that basically take the form of radical skepticism.)
Granted that god exists and cares about us and he can change the world, even in tiny aspects, it's very likely god will use those small aspects as a base to create the perfect world (kind of like AI FOOM). It follows that any world where god has some kind of minimum control will converge to the perfect world. Given that we are not in the perfect world, we can assume god does not have the minimum level of control.
Follow-up to: Every Cause Wants To Be A Cult, Cultish Countercultishness
One of the classic demonstrations of the Fundamental Attribution Error is the 'quiz study' of Ross, Amabile, and Steinmetz (1977). In the study, subjects were randomly assigned to either ask or answer questions in quiz show style, and were observed by other subjects who were asked to rate them for competence/knowledge. Even knowing that the assignments were random did not prevent the raters from rating the questioners higher than the answerers. Of course, when we rate individuals highly the affect heuristic comes into play, and if we're not careful that can lead to a super-happy death spiral of reverence. Students can revere teachers or science popularizers (even devotion to Richard Dawkins can get a bit extreme at his busy web forum) simply because the former only interact with the latter in domains where the students know less. This is certainly a problem with blogging, where the blogger chooses to post in domains of expertise.
Specifically, Eliezer's writing at Overcoming Bias has provided nice introductions to many standard concepts and arguments from philosophy, economics, and psychology: the philosophical compatibilist account of free will, utility functions, standard biases, and much more. These are great concepts, and many commenters report that they have been greatly influenced by their introductions to them at Overcoming Bias, but the psychological default will be to overrate the messenger. This danger is particularly great in light of his writing style, and when the fact that a point is already extant in the literature, and is either being relayed or reinvented, isn't noted. To address a few cases of the latter: Gary Drescher covered much of the content of Eliezer's Overcoming Bias posts (mostly very well), from timeless physics to Newcomb's problems to quantum mechanics, in a book back in May 2006, while Eliezer's irrealist meta-ethics would be very familiar to modern philosophers like Don Loeb or Josh Greene, and isn't so far from the 18th century philosopher David Hume.
If you're feeling a tendency to cultish hero-worship, reading such independent prior analyses is a noncultish way to diffuse it, and the history of science suggests that this procedure will be applicable to almost anyone you're tempted to revere. Wallace invented the idea of evolution through natural selection independently of Darwin, and Leibniz and Newton independently developed calculus. With respect to our other host, Hans Moravec came up with the probabilistic Simulation Argument long before Nick Bostrom became known for reinventing it (possibly with forgotten influence from reading the book, or its influence on interlocutors). When we post here we can make an effort to find and explicitly acknowledge such influences or independent discoveries, to recognize the contributions of Rational We, as well as Me.
Even if you resist revering the messenger, a well-written piece that purports to summarize a field can leave you ignorant of your ignorance. If you only read the National Review or The Nation you will pick up a lot of political knowledge, including knowledge about the other party/ideology, at least enough to score well on political science surveys. However, that very knowledge means that missing pieces favoring the other side can be more easily ignored: someone might not believe that the other side is made up of Evil Mutants with no reasons at all, and might be tempted to investigate, but ideological media can provide reasons that are plausible yet not so plausible as to be tempting to their audience. For a truth-seeker, beware of explanations of the speaker's opponents.
This sort of intentional slanting and misplaced trust is less common in more academic sources, but it does occur. For instance, top philosophers of science have been caught failing to beware of Stephen J. Gould, copying his citations and misrepresentations of work by Arthur Jensen without having read either the work in question or the more scrupulous treatments in the writings of Jensen's leading scientific opponents, the excellent James Flynn and Richard Nisbett. More often, space constraints mean that a work will spend more words and detail on the view being advanced (Near) than on those rejected (Far), and limited knowledge of the rejected views will lead to omissions. Without reading the major alternative views to those of the one who introduced you to a field in their own words or, even better, neutral textbooks, you will underrate opposing views.
What do LW contributors recommend as the best articulations of alternative views to OB/LW majorities or received wisdom, or neutral sources to put them in context? I'll offer David Chalmers' The Conscious Mind for reductionism, this article on theistic modal realism for the theistic (not Biblical) Problem of Evil, and David Cutler's Your Money or Your Life for the average (not marginal) value of medical spending. Across the board, the Stanford Encyclopedia of Philosophy is a great neutral resource for philosophical posts.
Offline Reference:
Ross, L. D., Amabile, T. M. & Steinmetz, J. L. (1977). Social roles, social control, and biases in social-perceptual processes. Journal of Personality and Social Psychology, 35, 485-494.