OK, I think I misunderstood your comment about 3' of crushed stone... I thought it went down to basement floor level, but on re-reading it looks to be a shallow amount of stone allowing water to drop down and pool just out of sight where the dirt starts next to the basement wall! I'd replace the stone with packed dirt (and grass or plantings) sloped away from the basement wall. Inspecting the condition of the sealer on the wall in the process...
Since your home is newer, the gutters may actually be connected to the local storm sewer which is fine (if not clogged)...
