Since we actually managed to get ourselves a new/reworked theme changed from the original prototype, I figure it might be useful to share what we did right.
We absolutely hated the original theme Super User had - and between my meta post (which admittedly would have been better if I'd calmed down at the time) and various suggestions from the community, we ended up with a theme with only the general generic complaints.
I was actually a little more gruff/angry in my post than I wanted to be but it really came down to what we disliked (default-ish theme, specific elements), what we liked on other themes, and what we wanted, and it worked out OK.
I'd also like to point out that, well, the designer is not going to have the same grasp of a site's "uniqueness" as someone who has been on it a while will have. I admittedly hadn't thought about that, when I complained, and itsit's probably useful if you need to put across why a specific design element is important.
I personally love the current theme we have, and it's only because we engaged and spoke up and let folks know what bothered us.
There's a few things that we did that worked great:
- Start complaining early: go through the mockups with a fine toothed comb. SU lost a lot of the design elements we disliked because we noticed and spoke up against them.
"This thing is terrible" vs. "This thing mangles up our logo"
or:
"The new logo is drab" vs. "Our site identity has always been designed around a two-color logo/robot"
- Focus on specific design elements you dislike and explain why you dislike against them.
We didn't like the 'filler' background on ours and explained why. I know a few sites recently complained about their backgrounds as well (though after release).
Especially where it's an item with emotive appeal, I'd still love to have sites retain the voting arrows and tags (and I do hope once there's a solid framework for new sites, this is revisited), and at this point I still feel strongly that this should be revisited at some point.
- Make it clear why you want certain things.
While it hasn't quite gotten a response yet (or a site design) - I love how Worldbuilding made a case for why Pandora and Slartibotfast should be kept. Its certainly better than anything I wrote for Super User.
Stuff that doesn't quite work...
Per-site metas have no reputation. Just... write an answer, in depth to why the current suggested themes don't work. Comments are just not the good way to do it. Getting angry isn't the best way to do it. Getting angry in comments is the worst way to do it.
Doing it after the new design is actually out kinda means folks already have it out after a consultation period. It means a lot of work getting duplicated, and there's a lot of sites to do. If you need something changed, do it as early as possible.