A lot of great input already but I wanted to chime in as well.
IMHO there is very little difference between 90% of the flies in the bonefishing universe. Pretty much all small and tan, right? Based on that assumption I've come up with a very effective way of maximizing the flies in my box. There are four main differences in my flies:
4. Attractors (legs, eyes, etc)
I agree that you want to tie up at least 6 at a time. I usually pick three sizes (4, 6 & 8). Then I tie them in three different weights (weight and size are, to me, the two most important variables). That's a total of 56 flies for all types of water.
Here is what I do that is a little bit different. I tie all these flies the same, including flash, eyes, and legs. I include EVERYTHING on the pattern. By having everything already on the fly, it only takes a small pair of scissors to adjust to current conditions and fish preference. Fish spooked because of the flash, take out the scissors and with a couple of snips the fly is muted and flashless.
I used to have the exact same problem you outlined at the beginning of this thread and this solved it. Let's face it, Bonefish are incredible pound for pound fighters, but are typically not the most selective fish in the world (I know some people will argue this, but as a gerenal rule....). As long as you know the basic patterns used on a given Island, this approach works.
Hope that helps