The problem is the human element. If you are doing something that can in some way be construed as going against the app store guidelines, eventually you are going to get a reviewer who rejects/takes down your app. Even if other reviewers knew that your app had been around for ever, you are eventually going to run into one who doesn't, or feels it's his/her job to be as strict as possible. There is very little consistency in Apple's process because of this. The company I work for has had apps rejected for things we've done literally about a dozen times before, and we certainly knew were border line but we figured were OK because it had been allowed so many times before. But eventually we run into a reviewer who for whatever reason, rejects something that we've done tons of times before.

Overall I think Apple's process works, but the inconsistency is just ridiculous. Especially when your releases are time critical.