Although the hardest part of the application is most certainly writing the code in the first place, the devil is always in the details. If your application does not install "normally" or put the GUI elements in the right place or respond to the correct keyboard shortcuts, your users might not be able to get beyond those little details to discover how useful and creative your application truly is.
Always consider your target users when you are getting ready for deployment of your application. If you can, test your application on each of the platforms you are trying to target. Even better, enlist a user who is not only familiar with that platform but also prefers that platform to test your application. He or she will be in a far better position to tell you about which parts that just "don’t feel right."