Faster waypoints download and upload

Hi there!
I’m writing my own mission planner specially for my purposes. One of things I want to implement is generating waypoints automatically. I have uploading and downloading waypoints, and did some measurements of time of it.
Mean time of downloading one waypoint is near 1sec, when I want to download few hundreds of them I got to wait some time.
Is there any way to fasten this? I saw in Arducopter source code that its waiting some time after reading waypoint from eeprom, and then before send it goes on some sending queue. I need to shorten this time. Is someone who knows why it takes so much?