What was he supposed to do, say Flash is horrible? He was supportive of his company's products; he will do that at Apple as well.
I would like to have seen Adobe publicly announce a phase-out of Flash for all computer browsers -- a hard line drawn in the sand -- and full encouragement of distribution of Flash through apps and in platforms' respective app stores.
I'd also like to see Adobe remove javascript functionality from their PDF reader. Having scripting available in Printable Document Format files has huge downside (malware) while having essentially no upside for anyone.
Flash Player and Adobe Reader are currently 2 of the 3 primary vectors for malware on Macs. Taking a stand to remove these vectors for modern computers would make PCs far safer and would be a huge PR move for Adobe. I don't quite know why they didn't do this; perhaps admitting the obvious security problems with Flash and their PDF reader would open them to liability.
And he obviously won't be working on Flash implementation at Apple (it's been dead at Apple for a while, and it's dying everywhere else).
I agree that Lynch would and should have nothing to do with Flash at Apple. At the same time, you should note:
Flash is not dead. Flash plays just fine with the app store model; Flash apps like Machinarium have done quite well in the various app stores. Flash runs just fine on Macs, iPads, iPhones and the iPad touch -- as long as the Flash apps come through the App stores. Adobe supports the distribution of Flash code through all available App Stores: Apple, Blackberry (RIM), Android, etc.
The evil is not Flash or Java;
the evil is the running of Flash/Java code in the browser. Distributing Flash/Java code through app stores avoids these problems. Simple.