Follow their suggestions and be polite. Even though you may disagree with their take on more subjective items like the usage of UI elements, take their advice and adjust your application to match. It doesn't matter if there's something that has been in your application from day one. I had a table view that improperly retained a selection when it shouldn't, something that had been in there from the launch of the App Store. When they pointed it out, I corrected the error and the application passed review a couple days later. Sometimes you really are the one at fault.
If after reworking you still receive a rejection and have no idea how to work around it, write an articulate, polite response to the reviewers asking for clarification and possible suggestions. Resist the urge to run out and start yelling to the world at large that Apple is specifically suppressing you and your innovation. That will only hurt you in the long run. Remember, there are real people at the other end of that From: address.
Anyone who's dealt with the U.S. patent system will find similarities here. Sometimes you get a patent examiner who picks apart every last element in your filing, and sometimes you get a patent issued with ridiculously broad claims. In both cases, you're dealing with organizations that have a huge volume of applications to sort through (although the patent office is far more restrictive). I've found that the patience and willingness to accept changes that works with one organization helps when dealing with the other.
Beyond all this, it helps to cultivate relationships with the people at Apple. They do want to assist you, and their engineers are extremely helpful people. WWDC is coming up and is a great place to get to know these engineers, as are the other Apple-hosted tech events. If you develop an advocate for your work within the company, that can definitely help with the review process.