If it's a PTH board the pad size should not be too critical, as long as you use good desoldering techniques, as the largest area of connection is inside the holes.
Most pad arrays on 0.1" pitch are sized to allow track between pads, which means the pad size must be restricted.
For prototypes that need frequent connections, use sockets!
I don't use Eagle, but in EasyEDA you can simply select all the pads and adjust the diameter and hole size of all in one go, then save the modified footprint.