Actually, Apple spends significantly less on R&D than both Google and Microsoft. They spend, but not billions like their competitors.
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.
Your whole image is based on non-engineer-driven products.
[1] Excluding the A5 CPU
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.
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.
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.