It is arguable that Apple was more innovative with technology prior to Steve Jobs's return to power. He dissolved the ATG, home of the original Cocoa, and Apple Data Detectors, and famously axed the Newton, continued development of which might have given us the iPhone as a platform years ago.
But the Newton's brand had been tainted by the poor handwriting recognition of the first models and a clunky form factor.
New (or returning) to Apple's innovation DNA is marketing. And I don't mean just advertising or PR, I mean making strategic business decisions to enter sensible markets that capitalize but don't dilute brands and have exploitable niches. Any student of game theory and business can appreciate that this is the real genius behind the 21st century's Apple.
Microsoft, meanwhile, has never really innovated in technology. They have, though, blazed a trail in business; it could even be said that Bill Gates established the practice of selling software. How disappointing that they've taken to trying to copy other business models with varying success; the Xbox, Zune, and Windows Mobile Smartphones are all me-too plays. MS has plenty of brilliant minds working on software, they need to get a few of them in strategic marketing.