hi,
MIM cap only preferred only in case of high linearity requirement. For decap i guess you don't have any such requirement.

Thanks.

yes, the gate oxide is usually thinner than the insulator in the mim.

If your process allows it, you can get maximum bypass cap density by laying out a MIMcap on top of the MOScap to make a bypass cell.  Be careful about the Q of the bypass cap, you may need to add a small resistor in series with the bypass cap.  To know, you will have to simulate with the expected amount of bypass cap and the expected inductance in the power rail.

usually for low noise design MIM is better. MOS CAP has higher noise than MIM

yes moscap makes good decoupling cap in terms of density, but as well as voltage dependancy, they leak current which is heavily temperature dependant.... this may or may not be a problem in your application.

One additional thought:
MOS caps have one of the plate capacitively coupled to the substrate, so what you have there are actually two capacitors in series.  You decouple two voltage supply rails but you couple one of them with the substrate through this additional capacitor.  So depending on the design you may inject noise into substrate (if that supply rail is noisy) or you may capture noise from the substrate into a sensitive supply rail.

Cosmin Iorga, Ph.D.
founder NoiseCoupling.com
http://www.noisecoupling.com