Never mind, I was able to make a simple C2 game work in Ejecta.
I had to do the following:
1. export as Html5 game
2. Modify runtime.js in the following places
a. set this.isDomFree = true and this.isiOS = true in function Runtime(canvas)
b. set this.ctx = global_ctx; in function Runtime(canvas). global_ctx is just an arbitrary global var that holds the 2d context obtained in the index.js script (see Ejecta documentation). That was the only way I could make it work, not sure why.
c. always return true in areAllTexturesLoaded. The loading progress logic did not work for me in Ejecta. As a ugly work aorund I just set it to return true. Obviously, this could create problems for games that load a lot of textures.
3. Create a index.js file for ejecta with the following contents:
var global_canvas = document.getElementById('canvas');
var global_ctx = canvas.getContext('2d');
ejecta.require('c2runtime.js');
// Create new runtime using the c2canvas
cr.createRuntime('canvas');
Please see Ejecta documentation for additional steps required for ejecta to work in Xcode.
As 
Ashley said, you need a mac to use Ejecta, but then again, you need a mac anyways when uploading the final version for publishing in the app store.
For me the biggest advantage of Ejecta over Cocoon or AppMobi is the already available integration with GameCenter. other than that, I think they perform the same. The other biggest possible advantage would be WebGL if 
vikerman is able to complete his amazing Ejecta webgl bindings.