In many ways the fossils thing seems like a bit of a dead end, for the very reasons you mentioned.
The discovery of some sort of direct message in the genome seems like a more usable device, but that is more in line with an old earth ID approach with continual genetic tinkering than YEC special creationism.
As I see it the main problem is that you can't really make your idea work unless you end up with some sort of last thursdayism or your fictional world operates on an entirely different basis from our own. Its easy enough to handwave away any evidence with the supernatural especially an omnipotent god, its much harder to come up with the sort of gradual accumulation of evidence you need for a satisfying plot. Otherwise you might just as well have Jesus turn up and tell everyone that the fossil record was just a joke.
I can see how you can have a satisfying story with an intelligent design alternative to darwinian evolution, but I can't see how you could have one with special creation in a world that resembled ours even remotely. I'm not saying you couldn't have that scenario, a modified form of last thursdayism again for example, I just don't see how it would make a satisfying or coherent story as you describe.
I think Brian Aldis's book Cryptozooic was unsatisfying in a similar way, the key revelation just made no sense at all.
TTFN,
WK
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