As I saw on the community we can use waypoints in different ways not only for movement characters or camera but also as points or to create ladders. So I think that it will be very helpful if we can set in WE color of waypoints for example green for ladders to make world more clearier and easier to find appropriate waypoints.

I second this. It's a good idea and would make it a lot cleaner.

Third.

And make Position Mode and Grid Aligning available for waypoints so you can more accurately and more easily position them.

Perhaps a snapping feature?
A toggle that will snap an object/waypoint to an object when it gets near? This would be great for creating a long wall or stacking a lot of boxs.
This in addition to Driklyn's suggestions would be nice.