The performance on mobile greatly depends on the type of device you are using. What kind of iPhone were you testing on? I have found that the iPhone 4 has pretty terrible results while the 4s runs MUCH better, and my new iPhone 5s runs flawlessly. Also any inefficiencies in your code (ie too many collision checks) will be much more noticeable when testing on mobile rather then on your desktop.
Other things to consider are:
How much memory is your game using? The lower you can keep it the better for mobile for sure, especially when using CocoonJS.
How many objects are on screen at once? See above ^
Is WebGL enabled? This gives a HUGE performance boost, but not all devices support it. It is definitely one of the awesome benefits of using CocoonJS.
Hope this helps