Hey Sarah!
What a great question! Let me first say that our family loves the
Disney Transportation System! Being a budget-conscious family, we appreciate the ability to save money by not renting a car. Another great feature is that your family will love being dropped off very close to the Disney Park Entrances, especially with a small child!
For my family, I always plan AT LEAST an hour to travel from any Disney Resort to any Disney Park. Some factors that will affect your travel times will be wait time for the bus, the number of guests waiting in line, the time you are leaving your resort, and even the "mood" of your family. If you have a Disney Dining reservation, I would give your family at least 90 minutes to leave your resort and arrive at the restaurant. Remember, you have to check bags before entering a park, get through the entrance of the park, AND travel to the restaurant. I promise planning for travel times will alleviate so much stress! With five kids, I know this first hand!
As far as the three resorts are concerned, I will tell you that Disney's Pop Century has its own dedicated bus transportation taking you to the Disney Parks and Downtown Disney. If your choice is to stay at a Value Resort, then I would choose Disney's Pop Century. If you decide to stay at Disney's Wilderness Lodge, then you have the option to travel by bus to the Disney Parks or by boat to Magic Kingdom.
If you have other questions, please let me know!
Have a MAGICAL day!
Wes