It's a tradeoff - for people who don't do much customizing they're trying to automatically place the most frequently used commands at the top. Probably works for 98% of the users.

It would be nice to give power users the ability to override these automatic decisions. They've done it in certain places on certain remotes but not everywhere. And yes it can be somewhat frustrating, especially when you're a former software developer and you know how to design it that way from the beginning.....