I think your ears are right on the money: acoustic pickups sound bad when recorded, even the better ones. Artists tend to have a bit of a vested interest in using the pickups, since they've paid for them!...and they're accustomed to using them live.

Try to persuade the artist(s) that the pickup tracks are not going to enhance the finished product. Acoustic guitars are just that--acoustic--and a good recorded sound requires that you hear not just the strings, but strings and wood and air all vibrating together. Only a mic can render that. Pickups are a necessary evil for many live situations. In the studio they're an unnecessary evil.

Good luck,
Brian

PS.--Sorry, you asked for suggestions and I gave you a rant, albeit a supportive one. Two things to try, if they insist on using the pickup tracks:

1) find and notch out the nasty, brittle attack frequency that nearly all acoustic pickups have. This will take some energy out of the high end, so you may need to compensate by adding a little gentle high shelving EQ. Or else just let the mic track carry the high end and use the pickup track mainly to add a little oomph down low, which is what acoustic pickups tend to be best at anyway IMHO.

Also, because pickups don't get the guitar top with all its overtones, they don't give you that lovely complex midrange that mic'd tracks get. One way to compensate for this might be to run the pickup track through an effects box set for very light chorus or detuning. This is definitely a less-is-more thing, but it's worth a try if the pickup sound is particularly lifeless.

HTH,
Brian

Here's a suggestion that has worked for me in some situations: I recorded the guitar to two tracks,one with a mic,and the other with the onboard pickup.I panned each track roughly 9 and 3 o'clock,and delayed the track with the onboard pickup around 15ms or so relative to the mic'ed track.This prevents the bright attack of the piezo from overpowering the mic and for some songs makes a nice full sound.