Lindsey,
Thanks for your question!
I don't think you will find it necessary to change resorts based on the travel times of the
Disney Skyliner. But I will let you make that call. Let's look at some of the estimated travel times;
To get from the Pop Century Resort to either park you will have to hop off your first gondola and switch to a second one headed to that particular park. If you were to move resorts, your travel times to Hollywood Studios and Epcot would drop from 12 and 20 minutes to 6 and 14, respectively. You would also save some added time, since you would eliminate that need to transfer at the Caribbean Beach Resort station.
For me, the saved time is not that notable, but you know what your 2-year old needs. You are basically saving 6 to 15 minutes, dependent upon Skyliner wait times. Either way you go, you are going to love the convenience of the Disney Skyliner, and the wonderful theming of either resort!
One added note. With a napper, make sure you ask for a resort room that does not face the main pool. The added noise level of kids on their afternoon swim break can make napping problematic.
Have a Magical Vacation!Doug