The progression for the penalties and bonuses is a direct consequence of how the XML works. The formula looks something like this:
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B*choose(N, S) - P*N
B is the bonus for holding a set, N is how many affected countries you own, S is how many you need for a set, and P is the penalty per country. "Choose" is the combinatoric function "N choose S". I can change the parameters (B, S, and P) but have no real control over the formula (or over who starts out with each country, neutral or otherwise). I checked with Lack before developing this, and he says that it shouldn't break anything as long as I'm careful.
Based on the comments that people have made, I think I'm going to go with B=2, P=2, S=2. That should be fairer than the first version, since starting with either one or two of them will give you the same deployment modifier, which means most players should be on the same initial footing.
As for darkness, I'm going for more of a black-humor feel than a genuinely dark feel -- sort of a post-apocalyptic "return to normalcy" kind of thing. Except with robots, mutants, zombies, and (of course) war on a massive scale. I'm working on adding some artwork that should help a lot with the feel; we'll see if that helps when I put up a new version.