I don't think the motive is to eliminate e-commerce sites as much as it is to fully monetize queries
Google asset's are more significant than SERP movements in the grand scheme of things. Those in large money making verticals would be aware of this.
When you hear Google saying things like " they don't prejudice search results in favor of making money for Google ", that's true, but it doesn't mean the page layout doesn't favor Google, where they definitely do favor income to themselves.
These updates, are designed IMO to eliminate the remaining organic slots from anything that manipulates a query. They are cutting off completely any low hanging fruit - anything that manipulates on any scale. Repeat "scale".
To safeguard the remaining slots, brands appear to have been promoted and maintained, and since Panda and Penguin require more refinement, they stay elevated until, presumably, the jobs done.
We probably loose site of the bigger picture when discussing the SERP's.