Here is my 2p. I agree in the long term phonegap/cordova will be great export paths, but at present the supported iOS export options are poor for older versions of iOS7 and below. I know a supporting factor for C2 to choose phonegap as its primary method to export to iOS was based on the quick speed of users upgrading to iOS7. However, iOS8 isn't being upgraded as quickly as iOS7 -> http://www.engadget.com/2014/10/07/ios- ... are-stats/ which concerns me as a developer for my short term* iOS releases.
*short term - I am hoping at longest we will have to wait until the next round of phone releases/iOS9 update. Which is probably another year away. Which is LONG time to wait.
What should developers do in the short term?
As I see it CocoonJS works now (or it did for me) so that should be supported as much as it can without changing the core philosophy of Ludei or Scirra's development paths. This means Ludei should provide detailed setup instructions and tutorials that is supported by both Scirra and C2. For instance at present there is no way to to showing loading screens between layouts, which is a big no no in game development (Check the major console developers TRC/TCR/Lotcheck documentation). So by default it should be turned off until C2 is willing to make changes to support it, which in turn depends on if it is a change they are willing to make. In other words whatever is exported from C2 just needs to work to whichever method is supported.
Scirra also need to remember that they state on their frontpage that they support publishing to iOS. Which attracts many developers to C2, me included. If they only want to support iOS8 then this should be stated on the front page. Otherwise I believe CocoonJS should be reinstated to provide full coverage. Yes, I know you have only depreciated the export option, but it leaves the question of if left unsupported how long will it continue to work?