Flies or flying...
I think what fish key on more than anything is the way a fly moves. Stupid (uneducated) fish - bones or tarpon - are aggressive and will hit a fast moving fly. They have no suspicion and will chase a fly down. As these same fish see more pressure and flies, they become wary and shy. Now, as you say, the presentation and the fly have to be right to hook up. Too much movement and they spook. I think they may be recognizing that unnatural movement.
I've heard several first hand accounts of the same experience you've had, and had personal experience with the bones here getting educated during the late 90's and 'dumb' again after hurricane Ivan. What I haven't seen is many folks that talk about fish refusing flies after experimenting with different retrieval styles. Most anglers have a particular way they retrieve for a given fish - some fast, some slow and long, some twitchy - and they stick with what they know works. Thing is, an aggressive stripping technique (i.e. moving the fly too much or too fast) hardly ever seems to work on educated fish.
This makes me think that normal bonefish pray moves very little and that when stripping for wise bones (or tarpon) less is more. Really. For example, in the FLA Keys tarpon are now way smarter than they once were. A lot of the guides are now teaching the 'dangle' stripping technique where once it was 1-2 foot strips. Same with bones. Some flats here you cast and strip, like for jacks but a little slower, and the bones chase the fly down to eat it. Other, more pressured flats require more of a soft-sell. You know, lead the fish a little further, and barely twitch the fly when they get into range. Watch the fish and you'll know if they've seen it. I've had fish study a fly for what seemed like a minute (probably 5-10 seconds) before tailing on it hard. The other fish that day spooked when the fly moved too much. I'm convinced letting it sit looked more natural - more like the behaviour of real pray and not merely like something he'll put in his mouth out of curiousity.
So, what's this to do with fly selection? Well, the more you're able to move a fly, the more impressionistic it can be. Take the Clouser - a top Andros fly. Big fish there like moving flies (feeding heavily on mud minnows and other baitfish) so the Clouser works great with long, slow strips. On the other hand, there are flats - say in the FLA Keys - that hold shrimp and crabs which hide rather than run, so you want to move the fly less. Of course, this gives the fish a lot more time to inspect the fly. Impressionistic flies or those with bright colors rarely pass inspection in a foot of crystal clear water under a bright sun. However, tie on a slightly more realistic pattern - no flash, neutral colors, and mono eyes - and you might convince him. Bottom line, the more you can move a fly, the less important fly selection is. The spookier the fish and the less you can move it, the better the pattern should be.
Finally, mix up the retrieve. On spooky fish I like little twitches - maybe 1-2 inches - but not too fast. Another good one is a long, slow strip and a pause. Both are very natural and have the advantage of keeping the fly in the 'zone' longer, basically requiring less of a decision from the fish than a fly it has to chase down. Many of the fish I cut my teeth on - fish I had to get clients to catch - were very smart and wary. I had to develop techniques and flies that would consistently produce. I use small flies, little or no flash, and neutral colors combined with a minumum of stripping to fool these fish. On my travels these same techniques have worked on spooky bones in Eleuthera, Exuma, and the FLA Keys... all fishing on my own.
Fly pattern is important, but it is rarely so simple as 'matching the hatch'. All the things mentioned in previous posts are certainly important: matching the color of the flats, weight of the fly, etc. However, equally as important is the relationship between fly movement and fly appeal. I mean, some flies work great if the fish don't get a good look - Charlies, Clousers, Gotchas - but don't work so well on smart fish when sitting still. Other flies work better sitting on the bottom - Merkins, Bonefish Critters, Vaverka's Mantis Shrimp, and O'Keefe's Turds. Those 7 patterns in various weights and colors will catch you fish almost anywhere in the world... if you move them right.
Boneheaded
PS Great question, by the way, Josko.