The headline of this post is more dramatic than the reality. Google is not actually making judgements about the design of your website. As Matt Cutts has said several times in his videos, Google doesn’t really care what colour your site is, what shape it is, how many H1 tags you have or the amount of text you use. All it cares about is promoting websites people want to read.
As I have said to many people on many occasions, there is an absolute logic to giving Google what it wants. Create a website that people can use, that people like to visit repeatedly, that people like to promote, that is textually relevant to the kinds of things your target readers search for in Google.
Following that logic, you don’t have to be an SEO expert to realise that a website full of pop-ups and advertising that gets in the way of the editorial will not be popular. Who goes to Google to say “please show me a site full of adverts”? (Except perhaps for someone doing a thesis for a media studies course).
So, what is it about web designs that Google is now judging? In Google’s announcement it specifically pointed to content with a “small amount of visible content above-the-fold or relevant content persistently (being) pushed down by ads.” As an analogy, think about the difference between a free local paper and one you pay for. The one you pay for is always better, right? Partly because the front page is not obscured by some huge ad for a bathroom or carpet company.
Google’s logic here is sound. Show people the sites that give them what they are looking for above the fold. Therefore, the advice for anyone is to take a cold look at your site through the eyes of a visitor. Are you giving them what they want or are you forcing them to see what you want?