I too have been designing battery operated devices for many years, parallel batteries are not my first choice. Operators can (and do) insert batteries backwards causing major problems, especially when using Lithium. Maximum life is achived when all batteries are same type (ie. Duracell) and age (ie. same box) even for serial configurations. I'm assuming that the motor will draw much more current than the MCU circuit, therefor I would optimize power for the motor (4 X 1.5v = 6V if using Alkaline). I would select larger cells (ie "D" instead of "AA") to get the required runtime. If Alkaline batteries won't do it, try Lithium.