I have one of the aforementioned Dean Markley pickups, recording directly into an old Tascam Portastudio 242, and the mix is punchy and bold. It's important to note that no matter how much tweaking you do, you can't fix a bad signal... but that said, it sounds to me like it's primarily an EQ/gain question. My experience has been that the pickup is a bit high-endy. I rotate the pickup itself (right in the soundhole!) so that it is farther away from the bridge at the high strings. Then I roll as much of the treble response as I can (couldn't tell you which frequencies.. it's all quite low-tech!
). I also reduce "mud" but cutting out as much of the bass as I can stand... which isn't much, because I'm a bass fiend!
What you're left with is fairly unremarkable, though. It's just a simple, punchy midrange guitar...
So if you want it to "shimmer" a little bit, double the part with a clean-toned electric guitar, single-coil if possible... and then just hide it in the mix a bit. Don't treat it as a second instrument on the track, just fade in enough that the track gets some texture.
If you don't have such a guitar, you can always record a second acoustic track and then mix it softer and with a bit more response in the high frequencies.
As a final note, vary your attack on the second track where possible... even if you double it as accurately as you can, there will still be a difference, and the texture will show... but the occasional 'suprise' will add a bit more dynamic to the track.
That's it for me... caveat emptor, though, I just do what seems to work.