The first reason, that comes to mind, is roughness. But there are two opposite points of view on it:
1) It could increase capacitance because of high electric field on the ends of cones forming rough layer
2) It could decrease capacitance since it decreases contact area between electrode and dielectric.
It seems that for the solid dielectric layer the second point is right. But according to e.g. G.Rebeiz "RF MEMS Theory...." 2003, p.93 fig 4.2(a) this effect provides only about 0.75 ratio between ideal and rough capacitors, but in my case this ratio is about 0.5 and sometiems lower.
Please, help me to understand this effect of high mismatch between calculated and fabricated capacitances of RF MEMS capacitors.