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Once the co-owner of the powerful “Wintel” monpoly, in the past decade, Microsoft (NASDAQ:MSFT) has been suffering an increasing slide towards irrelevance. The onetime brash PC pioneer has looked more and more like a legacy software company protecting an installed base.

Nowhere is this trend more painful than in the mobile world. Since 2006, it has never held more than 15% of the global smartphone market and in fact — under the twin onslaught of iPhone and Android — its market share has been in a freefall, giving up more than three-fourths of that share. To add insult to injury, 2011 was the year when more smartphones shipped than PCs, a trend that’s only going in one direction.

To save its mobile strategy, Microsoft’s put all its money on its Nokia alliance in hopes that would save Windows Phone 7 from the same ignominy as its predecessors. Given that Nokia’s (NYSE:NOK) share has also been in freefall, this has the potential of extending Gary Hamel’s “two drunks” analogy from acquisitions to joint ventures.

On Tuesday, Microsoft landed a public endorsement from one of the mobile industry’s most powerful players: Qualcomm (NASDAQ:QCOM). To me, this has the potential to be the most powerful ally that Microsoft could attract, as a net positive for both firms and a negative for their respective rivals, Apple (NASDAQ:AAPL) and Intel (NASDAQ:INTC) (and to some degree, Google (NASDAQ:GOOG)).

At the company’s annual shareholders’ meeting, Qualcomm CEO Paul Jacobs bragged a little about the company’s successful shift of its semiconductor business from radio modems (“basebad processors”) to its Snapdragon all-in-one process — which include an ARM-compatible CPU, radio, graphics, multimedia and other features. Based on its Snapdragon success, Qualcomm has continued to gain market share, passing TI last year to become the leading supplier of cellphone CPUs (“application processors”), according to Strategy Analytics.

(By not making its own cellphones or infrastructure, Qualcomm also had a unique position in the mobile phone value chain. Instead, it devotes its $3 billion/year R&D budget to developing components and basic technologies that it sells to all comers among the various handset and platform providers).

Qualcomm has two reasons to throw its weight behind Microsoft. First — unlike Android — it’s the only game in town, as the sole CPU supplier for WIndows Phone products thus far. Secondly, Qualcomm sees Windows-on-ARM as opening a whole new market — allowing it (and other ARM licensees) to take CPU market share away from Intel in the PC and tablet space.

In Jacobs’ view, the Windows-on-Snapdragon (or — as I put it, “Windragon”) combination will merge the office productivity options of Windows with the mobility, power saving and performance of the Snapdragon CPU line. Part of the shareholder meeting was devoted to demonstrating the Snapdragon S4 processor designed for the Windragon market.

This sort of tight alliance would seem to me to accelerate the estrangement of Apple and Qualcomm in the handset world. A shareholder asked when (or why) Qualcomm can’t provide more chips to Apple, which appears to be limited to its baseband processor (in the iPhone 4 and iPhone 4S) to complement Apple’s own A5 ARM cpu. If Qualcomm is going to help Microsoft gain share against the iPhone, iPad and perhaps reverse the OS X gains against Windows, then the Apple of Steve Jobs (and perhaps Tim Cook) is not likely to be too friendly or dependent on the San Diego chip giant.

Certainly success of Windragon would accelerate the shift from Mac to iPad sales and Apple’s expected phase-out of OS X.

The other interesting implication is what it does to Intel. There’s no love lost between the firms, particularly in the WiMax vs. LTE 4G wars (that Jacobs alluded to Tuesday). At the same time, Intel is suffering from the same shift away from PCs that threatens Microsoft.

Will Intel make ARM-compatible CPUs, as it once did? Will it try to more aggressively win Android allies to counter the Microsoft-Nokia-Qualcomm alliance?

Disclosure: Author has holdings in INTC.