It looks like someone suggested a non-Flash eManga reader before, but with Apple coming down on DMP content in the iTunes store, maybe there is incentive to open this subject again.
You know how some websites have mobile versions for smart phones and tablets? Could eManga do something similar so that we eliminate the need for third party apps? You could simplify it down so it's just a login, a list of purchased titles, and the ability to read one page at a time that has been resized for a smartphone or a tablet. I wouldn't be surprised if there is already a framework in existence for pushing images to iPhones and tablets.
Also, it stops the middle man from taking a piece of the profit pie