Can you give an example? The only issue I've ever had with ABP et al. is when I'm working on a site and forget to turn it off & I think my site is broken (because ad doesn't load). :p
One of our webdevs complained about some issue that was causing issues with our site in particular (regarding generic id names being blocked) and since then I've had several anecdotal instances where disabling adblock on sites seems to clear up nagging issues.
I haven't found a significant example of this, and I've been browsing with Adblock Plus for years. The only place I've seen issues with is some video streaming sites, when it interferes with streaming ads.
Doesn't Adblock Plus alter the structure of the page, which can mess up layout?
Also believe it or not I don't want to block all ads, just animated ones. I want a general solution for All People, not just us nerds, and erasing advertising from the web would destroy a lot of businesses.
I want something browser makers can build in and turn on by default, which is what Safari has essentially done now with Mavericks (Flash and Java are blocked by default.. Flash under the rubric of power conservation).
There's a setting in ABP for Firefox that allows you to show "placeholders of blocked elements". I think that's what you're after if you want to use ABP and maintain the layout?
Maybe a crowd sourced blocker would be ideal for identifying divs in a site.
It would be a plugin that allows you to mark a spot on a page that is an ad and the plugin will record the very specific CSS path and hide it permanently for you and others that go to visit that site.
Maybe once you have a significant number of CSS paths you could do something with machine learning to identify the likeliness of a div containing an ad and block it when it crosses a certain degree of confidence.
I think an domain blacklist a la Adblock is probably the best idea but that won't help you with ads that are already present in the DOM on pageload.