R&D != patents.
The number of patents generated by a company is really based on the system employed within the company and not about how innovative the company is. Most software patents are bogus and if your company is set up with a great system to file patents quickly then you will get a lot of them. For example in my company, your performance is based on how many patents are filed. Additionally they have an entire team of lawyers that take any one page description of text and turn them into patentable items. The team of lawyers write the patent, do the research on prior patents, and will then file the patent for us.
It's a great patent filing system and it generates A LOT of patents, but the company is definitely not innovative.
Most other companies that are less keen on such a system will not file these bogus and broad patents.
When you're mostly creating a better case, better UX, and better marketing.. and your partners do most of the really hard low-level technical stuff [1].. why bother with R&D?
Your whole image is based on non-engineer-driven products.
Really? Do you think making an OS (Mac OS X and iOS) and all the hardware designs of their dozens of products (remember airport express, iPods, macbook air, etc) are all "easy" to develop? Mac OS X and iOS are based on BSD, but they have been hugely modified. In fact, the kernel is far from BSD now, and they release it as open source Darwin -- it has influence from other OS'es as well.
Almost all of the difficult underlying technologies in Apple products were created 10-50 years earlier by other companies and government agencies such as Intel, Xerox, NASA, Qualcomm, the US DoD, etc. They are basically the world's most famous system integrator. If you still disagree - let me reflect the question: list the fundamental, widely accepted contributions that Apple made to cutting-edge EE/CS research between 1990-2010. And compare that versus NASA, Microsoft, Intel, etc.
Apple is like that apocryphal hot girl in high school who got the nerds to do her homework. Due to her popularity - it's almost impossible to question her intelligence without bringing a world of hurt down upon yourself, yet despite her good grades and high social status, she isn't generating very many fundamentally new ideas on her own.
Then why compare Apple with these companies? Compare them with other systems integrators and product people like HP or Compaq or Gateway, etc. Apple does manufacture the most competent desktop environment available, even if the core is open source, they made all the desktop GUI and the dock that every OS (including Windows 7) is now ripping off. HP never managed anything like that.
Besides, clearly the UX, making the better case, and the marketing, etc. is actually the hard part, because there's dozens of companies making chips. There's only one out there releasing Apple-level consumer goods.
Thats a percentage of revenues, and Apple's revenues are very high. Also -- I agree Microsoft spends a lot of money on research in their "Microsoft Research" division, but the fact is, most of their research does not end up in products. I don't know about Google - I don't think they spend a lot on Research...the link you pointed to does not talk about Google. :-)
Microsoft is a six-barrelled shotgun to Apple's sniper rifle. Chances are, Microsoft will hit something. Whereas Apple's recent misses are so few as to be individually noteworthy.
Sure, I don't mean to commend them on their efficiency ('bloated'), but they have a startlingly wide offering of software. It's not limited to just Office and Windows de jure.
I don't really think it's fair to compare the R&D budgets - there's a lot of difference - MS has an extremely broad array of software (multiplied by i18n), while Apple has an extremely vertical stack of products. I don't think these differences can be hand-waved as being theoretically financially equivalent.
It's a great patent filing system and it generates A LOT of patents, but the company is definitely not innovative.
Most other companies that are less keen on such a system will not file these bogus and broad patents.