The $900 would be the decision-maker for me, so it might also color my advice, BUT I'd say stay at POP with a rental car. First, $900 is $900, and it'd buy a lot of character meals, etc, for your family. It's nice to have the car for grocery runs, off-site meals, and NOT HAVING TO RIDE THE BUS. If you are at POP, you can park fairly close to your room, depending on the building, and won't have to walk across the resort to get the bus. Regarding MK... I know that people think the monorail/TTC/parking tram is a hassle, but we consider it part of the fun! Where else do you get to ride a monorail? Also, I read that the monorail repairs are supposed to be finished this month, so I'd hope they would be running more regularly moving forward. Another way around the monorail/TTC issue is to use UBER to the Contemporary on your MK days and then walk between the CR and MK. You'd have to pay for the UBER, but it'd keep you from using the monorail/TTC multiple times a day. Maybe only do the UBER option for nap time? OR if you have park hopper tickets, you could rope drop MK and go back to the resort for nap time (having used the bus), and then drive to the evening park. That would also cut down on your transportation time, even if you drive yourself to MK instead of busing or using Uber, and hopefully your kids would be awake when leaving MK at lunch time- and the buses aren't anywhere near as bad as at park closing- so you wouldn't have to ride standing up, holding sleeping kids.
I'd somehow make POP work. $900 is a lot of money to save!