Apple filed its annual 10-K report with the SEC on Wednesday, and the numbers include a significant increase in research and development expenses, growing $952 million—now $3.38 billion from $2.43 billion last year, an increase of roughly 40%. The company now has 72,800 full-time employees, and 390 retail stores averaging $51.5 million in annual revenue. It expects to open 30 to 35 new stores in 2013, “with approximately three-quarters…