The problem with this design, the reason you still encounter significant opposition in spite of the many adjustments, is because it's still too reminiscent of the old conspiracy theory-themed design.
Sean put great attention to details in the original designs. The choice of font, the paper-looking dirty white background color of the central column, the squareness of the buttons, the big black line dividing section, excessive amount of whitespace, the understatement of links, etc. All of it serve to reinforce Sean's initial desire to represent the analog version of the site, "like the wall of a researcher or reporter trying to connect the dots on their fact finding mission."
If we were to analyze the design based on whether Sean succeeded in bringing that feel, we would have to give it full marks. Sean succeeded in creating the mood he desired.
Unfortunately, that mood was rejected by the community.
In response to the feedback, Sean removed the most glaring offending aspects of his design in the hope that it would make it palatable to us. Fair enough. If the design had been only slightly altered, that might have worked. However, the flaws run deeper. Sean clearly put a lot of time in this design, and since his intent is not compatible with the community's preferences it's still causing problems. Most of the negative reaction you see to the design are symptoms of this larger problem.
Another way to phrase the problem is that Skeptics' design looks a lot more like English's than Physics'. You would expect a site about scientific inquiry to share a lot more commonality in design with a site about physics than one about the English language.
That's not all.
English's is an exception in the Stack Exchange Network, not the rule.
When you look at graduated Stack Exchange site, most of them share this very polished, minimalistic and modern look. English does not. It breaks the rule for the right reasons, though. The design emulates a specific mood that is a solid match for a site about the English language.
The community does not desire special treatment. Quite the contrary, in fact, we want a design that is more in line with other graduated sites and the new beta theme.