I agree these methods still require a fair amount of expert knowledge and intuition in order to make the various choices you mention. On the other hand, Bayesian optimization can prove useful for exploring such a space. A recent paper (http://arxiv.org/pdf/1206.2944.pdf) used Bayesian optimization with GPs to find hyperparameter settings for a deep convolutional network. The resulting hyperparameters gave state of the art performance, beating those chosen by an expert (Krizhevsky, the researcher who recently won ImageNet).
Given that pharma is a massive industry and that drug discovery often costs around 1 billion dollars, the top prize of $22,000 seems awfully low. Will we start to see larger prizes, or will startups take this technology and monetize better than academia currently does?
What? Why don't they consider themselves part of Google?