So if I go with Serial to communicate with the 2 MPU's I can still use one for I2C for things like ADC's or Temp sensing?
Yes.
So I guess now the question becomes is it harder to use both Serial for the MPU's to communicate and one of them I2C or just do all I2C?
That may depend on how good the Arduino I2C library is at being a slave. I have no experience with it so can't say.
If that works I'd say use I2C for everything, and that frees your serial port for talking to a PC or for programming.
Rob