This article makes a deeply flawed assumption by including "outside" patents, that is to say, patents which were acquired (rather than developed/filed/patented by the company's own employees). Notice this tidbit disclaimer buried towards the end of the article:

"In Google's case, we get a clue. One of the company's largest super inventors lives out there, in the periphery, disconnected from other products. That inventor is Kia Silverbrook, who sold the company 269 granted patents on cameras and printers in 2013. Obviously patents that have been recently acquired, rather than developed in house, would lack the interconnections with other employees that centralize the largest bubbles."

This is not a clue. This is a sign that you're biasing your sample. Compare this statement to the premise of the study:

"Over the past 10 years Apple has produced 10,975 patents with a team of 5,232 inventors, and Google has produced 12,386 with a team of 8,888."

Wrong, not all of those people were even employees, see above. And what about the huge patent purchase Google made by buying Motorola and then selling it off (Arris, Lenovo) while keeping the vast majority of the patents. [0] Is it accurate to count Motorola’s patents as Google-developed innovations? Is it accurate to group Motorola inventors along with Google inventors?

"This seems to indicate a top-down, more centrally controlled system in Apple vs. potentially more independence and empowerment in Google."

I disagree, this really doesn’t indicate anything and mis-characterizes the inventors. Google and Apple have purchased a sizable number of patents whose inventors are not employees and not involved in Google's or Apple's R&D. If anything, this may indicate that Google purchased more outside patents than Apple. Some examples of Google's purchases beyond Motorola are IBM [1], Silverbrook [2], IP3 [3]. One of Apple's biggest set of outside patents is Nortel [4].

"Google, on the other hand, has a relatively flat organizational structure of many small teams filled with empowered individuals."

Not disputing this but the more obvious explanation is that Google has been working on a wider variety of products and services than Apple which would mean a greater variety of patentable subject matter by inventors working in different technologies. Don't use patents or that visualization as any indicator of R&D organizational structure.

"But that would take further sleuthing to confirm."

In the patent search community, it's pretty easy and quick to filter a search to only include company-invented patents (it's as quick as filtering down to a specific company, just compare latest assignee to original assignee). So why not do that here? This is such a simple search that I'm surprised that the data provider "Portland-based data visualization studio Periscopic" didn’t team up with any of the dozens of patent analytics providers [5] who probably would have done the work for free for some publicity, not to mention address the glaring flaw of including outside patents (that is, non-employees as inventors).

"Our intention behind PatentsView was to create interfaces that could inspire the public to explore patent data," says Periscopic cofounder Dino Citraro. [...] Indeed, Apple and Google may only be a start. You could probably write a book on the corporate organizational structures revealed in PatentsView."

I hope no one uses this tool to write a book. I think it's a noble goal to open up the data and visualization to the public, but users should be very wary of what they’re really looking at.

[0] https://en.wikipedia.org/wiki/Motorola_Mobility
[1] http://www.iam-media.com/blog/detail.aspx?g=54821371-e57d-47...
[2] http://web.archive.org/web/*/http://www.seobythesea.com/2013...
[3] http://www.prnewswire.com/news-releases/calling-all-patent-o...
[4] http://www.reuters.com/article/rpx-rockstar-ip-idUSL1N0U713M...
[5] https://www.piug.org/vendors