Those would, indeed, make for a better reference book. No argument there. But I don't their presence defines a reference book.
Fair enough.
But IMHO, even without making the PHB the ne plus ultra of reference books, it has discernible room for improvement just to get it to the level of some previous editions.
To me, dividing the PHB into distinct chapters for (in no particular order) races, skills, feats, classes, combat, equipment, magic items and powers/spells, with a nice glossary & index would have been better. That's more or less what previous editions (and many other games, FWIW) have done. If you don't care for the way 3.X grouped them all alphabetically, with little lines about which class gets them at what level, you could just as easily adopt the 1Ed type layout, in which each class' powers get a separate subsection, organized by alphabetically & by level.
But the 4Ed book folds the powers & spells into the character class section- and it does so in a way that you can go for pages and pages without seeing anything BUT those powers & spells. As I've stated, its a mess to me and others, and I honestly feel it slows down the "research" process of looking through the classes and powers for something in particular.
I hate to say it, but it actually reminds me of the way Palladium lays out RIFTS and other Palladium system game products.
In addition, key terms & symbols are defined dozens of pages away from their initial use. That's sloppy. In 3.X, you'd often get a definition within a paragraph or 2, or a sidebar. I found very little confusion of that kind in 1Ed or 2Ed.
(Yes, I know that there are exceptions- some quite egregious- and I've commented on those elsewhere.)