After reading the comments and discussing with Wulf, I wanted to give everyone a quick breakdown of the direction we are leaning towards.
Revised Stat Blocks
Each creature's stat block will be revised, as discussed previously. In the PDF, each creature will get its own page for easy printing. We also will include bookmarks and hyperlinks to sort alphabetically, by type, CR, and possibly even by "spine value".
The print version will be laid out alphabetically (although I made a case by type). We would like each creature to get its own page but that is TBD depending on page count and layout. If not, the entries will be per column.
Advanced Creatures
We are going forward with a "hybrid" of the various options Wulf and I presented in this thread.
Advancement by HD
For these creatures, we will stat out selected advancement "break points". Most likely, these entries will be every 3 or 4 HD or CR.
For example, we may include stats for an aboleth with 12, 16, 20, and 24 HD or at CR 11, 15, and 19. This may be an abbreviated stat block so we don't repeat info.
This is much more practical than just including massive tables for each monster or monster type. It gives the DM a variety of options for each creature that he can use and bring to the table quickly.
Advancement by Class Level
For creatures that advance by class level, we are going to stat three "paths" - heavy striker (warrior, solider, etc), light striker (scout, rogue, etc), and caster (shaman, witchdoctor, etc) - again, at various "break points".
When the dice start rolling, the class levels you used to create your NPCs don't really matter, only the modifiers do. This system will allow DMs to define general roles for the creatures he needs and stat them quickly.
Both of these methods, in addition to the Quick Template system that we've discussed should give DMs a multitude of new ways to customize monsters quickly and easily.
The "Ur-Monster"
As Wulf described on the previous page, this is a generic monster template that DMs can use to create and stat out completely new and unique monsters quickly. Rules for adding special abilities, types, and size will be included.
Quick Templates
This section will list all the quick templates, recommended creatures and types, and perhaps some random tables.
Traps & Skills Challenges
still TBD