Chief Executive Tim Cook’s third big hire after the short-lived Mark Papermaster (during Steve Jobs’ second leave) and unpopular John Browett is former Adobe CTO and Flash advocate Kevin Lynch, who will report to the SVP of Technologies Bob Mansfield. It would seem Lynch is pretty set up because Mansfield is set to retire next year and Lynch carries the same VP of Technologies title.

The hire seems to be a very interesting choice, however.

Lynch is a long-time Adobe veteran who came over when the company purchased Macromedia in 2005, largely for its Flash technology. Interestingly, Apple SVP Phil Schiller was the Vice President of Product Marketing at Macromedia, Inc. from December 1995 to March 1997. Lynch served as President of Macromedia Products and then as General Manager of Web Publishing from February 1996 to June 2000. The two likely spent some time together, although it was admittedly a decade and a half ago. Still, the relationship seems to be cordial.

However, Lynch’s recent dealings with Apple haven’t been so friendly…

Jobs’ ‘Thoughts on Flash’ called out many problems within the Flash software that Lynch was responsible for, including: reliability, security, performance, and battery life problems.

Symantec recently highlighted Flash for having one of the worst security records in 2009. We also know first hand that Flash is the number one reason Macs crash. We have been working with Adobe to fix these problems, but they have persisted for several years now. We don’t want to reduce the reliability and security of our iPhones, iPods and iPads by adding Flash.

In addition, Flash has not performed well on mobile devices. We have routinely asked Adobe to show us Flash performing well on a mobile device, any mobile device, for a few years now. We have never seen it. Adobe publicly said that Flash would ship on a smartphone in early 2009, then the second half of 2009, then the first half of 2010, and now they say the second half of 2010. We think it will eventually ship, but we’re glad we didn’t hold our breath. Who knows how it will perform?

Fourth, there’s battery life.

To achieve long battery life when playing video, mobile devices must decode the video in hardware; decoding it in software uses too much power. Many of the chips used in modern mobile devices contain a decoder called H.264 – an industry standard that is used in every Blu-ray DVD player and has been adopted by Apple, Google (YouTube), Vimeo, Netflix and many other companies.

Although Flash has recently added support for H.264, the video on almost all Flash websites currently requires an older generation decoder that is not implemented in mobile chips and must be run in software. The difference is striking: on an iPhone, for example, H.264 videos play for up to 10 hours, while videos decoded in software play for less than 5 hours before the battery is fully drained.

Not quite an endorsement of Lynch’s work. Lynch penned his own ‘Moving Forward‘ in response.

We feel confident that were Apple and Adobe to work together as we are with a number of other partners, we could provide a terrific experience with Flash on the iPhone, iPad and iPod touch.

However, as we posted last week, given the legal terms Apple has imposed on developers, we have already decided to shift our focus away from Apple’s iPhone and iPad devices for both Flash Player and AIR. We are working to bring Flash Player and AIR to all the other major participants in the mobile ecosystem, including Google, RIM, Palm (soon to be HP), Microsoft, Nokia and others.

We look forward to delivering Flash Player 10.1 for Android smartphones as a public preview at Google I/O in May, and then a general release in June. From that point on, an ever increasing number and variety of powerful, Flash-enabled devices will be arriving which we hope will provide a great landscape of choice.

What’s really interesting is that Apple’s contention about Flash is that it was bad software. Too buggy to go on iOS devices. Lynch was the guy responsible for Flash.

Adobe killed Flash for Mobile in November of 2011, just after Steve Jobs died, and it’s rare to find it on mobile or even tablets since the other big player Google has mostly abandoned the technology too. As Adobe moves away from Flash and to building tools to make HTML5 websites, Lynch may have found himself losing power and credibility in the organization.

But, in a strange twist of fate, he finds himself at Apple—the company that likely put the dagger in his Flash baby. From this angle, it is hard to see the logic in this choice.