Design considerations for micro dc to three phase ac AVR based (ESC) for miniature UAV applications
When using high-side N-channel MOSFETs, a MOSFET driver chip is generally used (e.g., an IR2130). These chips require a boost capacitor which allows the gates of the high-side MOSFETs to be driven with the required voltage. The downside of this is that the MOSFET driver has a restricted operating range (typically 10V-20V). The second down-side is that you can't drive the MOSFETS to 100% pulse-width; this is usually not a problem. Alternatively you could use P-channel high-side MOSFETs and N-channel for the low-side. With this configuration, you can PWM the low-side switches only and save some power. (You can do this with all N-channels as well, it's just trickier since you have to keep the boost capacitors charged). Go to Digikey and search for "mosfet driver", you'll want the 3-phase bridge drivers specified for external switches.

As for the MOSFETs themselves, I don't recommend you use them in parallel. This would increase your footprint as well as your gate charge. Instead, look for high-current mosfets on Digikey. My favorite packages for these are D-Pak, 8-PowerVDFN, and PowerPAK 1212-8.

Atmel has an app note for sensor-based and sensor-less motor control. Unfortunately AVRs don't have much processing power and your control algorithm will likely be restricted to fixed-point math because of this. Because of the processing power limitations, you may want to consider not using the Arduino environment and instead use straight C or assembly.

You may have some trouble isolating the I2C bus optically since it's a bi-directional bus. If you were to use a communication system with single direction lines, you may want to look at TI's line of isolator chips (e.g., the ISO7221).