I'd prefer to stay with the Mega, modified to operate at 3.3V. Really, the only bad thing in the modification will be replacing the fuse with a diode, but shouldn't be much of a problem since the computer USB port has current limits.
For this project I need the 14 digital output pins, the 2 I2C lines, as well as 14 PWM outputs for servo motors I'll be using.
Also, I unsoldered all the sensors and tested each - all of them work perfectly and don't seem to have been affected by overvoltage. So, why didn't it work? As long as it doesn't break the sensor, 5V and 3.3V application should be practically the same, right? Or does the MPU6050 only respond to 3.3V signals?