In this modern age of pnp rules (and of course the brilliant 2ed downloads) I do think that putting everything into one file is not the best way to handle the release of rulebooks. My suggestion is to split them up in a logical and practical manner.
The Rules
These are the pages that you are most likely to print out and will be the most useful at the gaming table.
The Scenarios
These are only needed when played. I mean, why print out a scenario that you've never played?
Unfortunately the arrangement of the scenarios, such as having them span multiple pages, doesn't help. A page should include 1, possibly 2 scenarios and if that leaves white space, so be it. A scenario can then be printed out when required (and then stored).
The Ships
S1 had a scenario's ship details included with each scenario. S2 gave a complete ship listing at the start and then had each scenario specify the ships to use. Both of these methods can be bettered.
Basically, each scenario has a page (in a separate booklet) for the ships used. When that scenario is played, the ship page is printed out giving you the exact ships needed in a form that is ready to use. It doesn't matter that ship details will be repeated in different scenarios, that just makes the file slightly bigger. All that matters is that with a couple of pages printed out, you're ready to play the game.
Cheat sheets
I always prefer these to be in separate files so I can refer to them whilst reading the rules on my PC.
The important thing to remember is that pnp is a different medium, that electronic files are more easily produced and that players don't need to print out stuff that they don't need.