One of the features of the Alpha 3 book I liked the most was the Designer Notes boxes. I would actually like to see some of these, or something like these in the final release of the game.
Insight in to the design process of a game can enhance play experience. Knowing why a certain decision was made, or in may cases, what options were considered can give a better understanding of the game, and grant new ways to look at different abilities and rules.
My favorite part about the designer notes are the ones that list different options for a given mechanic, and the request to try them out, and see which works best. Why only pick one to be in the book? If different ways create a different feel to the game, but don't drastically alter mechanics, why not let players and GMs pick the one they want? Starting and level up HP have always been a headache for players and GMs alike. How many campaigns has everyone here been in that started at level 3, because nobody likes being a squishy for the 30ish encounters it takes to get to a hit point total that isn't laughable? Well, we now have 5 different ways of generating starting hit points. Each of them plays to a differnt feel in a campaign. I like the racial HP bonus, because I think it's flavorfull. A munchkin in my group like the Constitution method, because he gets to be a small tank at level 1.
The skill revision notes give an excellent insight in to what has been an ongoing issue with the game system. This is good example where a descision had to be made, because so much relies on skills. The justification for the choice, and the adaption for prestige classes offered are also a great help to players and GMs converting their campaigns or using non Pathfinder source material. Using the Designer Note within the rules themselves places these things in a nice sidebar for quick reference, and has some insight attatched to it.
I'd like to see some of the designer notes left in the finished product. They wouldn't need to be labled as such; call them something like Worldbuilder Notes. Whatever. The important thing is they are a good way to include clarifications, adaptions, examples, insight, and general information that wouldn't fit in with the normal flow of the book.