Sensing capacitance changes this small is very difficult, as you know.  This
difficulty has driven MEMS sensor companies (such as Analog Devices) to
integrate their structures and circuitry on one chip.  Any other approach
leads to gross errors in measurement.  The circuit topology which monitors the
structure is the second most important issue.  I am an independent consultant
specializing in this area.  Please check out my web page,
MicroMechatronics .
For further discussion of this issue I can be reached at (608)741-0547.

Regards,
Mike Mattes