A better index in general would be great.
I noticed that I really love the DM Screen for 4E. It contains most of the information I need at the table - unfortunately, I don't have it when I am running my online campaign, so I reference the PHB, and that is fast, but not as fast as the DM Screen.
Sometimes I think that for better reference use, it makes sense to provide the same information twice, in different layouts. The "learning the rules layout" where you move through it step by step, and the "quick reference layout", where you have all conditions and options layed out on one or two double pages. Of course, that might "anger" some people because they feel like they paying twice or something, but.. people will always find something to complain.
Regarding the "learn to play" - I think it would be helpful to have a few more gameplay examples. The problem of course - when used as a reference, these make the rules harder to find since some random amount of gameplay examples are spread through. But then - repeating information like I mentioned could help this. The gameplay examples would be spread between the combat rules chapter, and maybe at the start or end of the power explanation stuff.
I am not sure what (else) would be useful for better "reading" (vs. referencing). I guess I am not the kind of guy that reads rulebooks that way most of the time. Maybe a little more space reserved for fluff? For example, one could have the classes chapter started with a short overview of the classes and follow that with a section of these classes acting in the gameworld - a party running through an encounter, without referencing the rules. At a later point, when using a game example, one could refer back to the party.
I kinda miss the "iconic" party, too. Or rather "iconic parties". 2 parties, covering all classes and races in between. The party is described by names, classes, and a short introduction who they are, how they got together, what they are going to do. (One could reference the KotS and the DMG adventure as "hooks"). It would also be cool to have these party reappear with illustrations describing them at paragon and epic tier. This could also happen in supplements. Martial Power 1 describes the martial heroes at paragon tier, and Martial Power 2 at epic tier. And their storyline could also continue, perhaps refering to adventures that have been released since then (avoding too many spoilers), or just some made up stuff.
All this stuff is mostly useless at the gametable, but it is nice "fluff" and makes it more entertaining to read, I think. It's give some time to "relax" from learning the rules and understanding the game to just think about what kind of adventurers these guys could make.
I am actually tempted to write such a "iconic party" up.
Of course, all that would blow up the PHB by a few pages, and especially the iconic party would require additional illustrations, probably by the same illustrator, if the iconics are to be repeated in different contexts.