You could skip points with small distance changes, what might be better would be to skip points where the elevation is greater than the distance change. That would be walking up a slope greater than 45°. I guess anyway you do it, you might have to play around with the limits on your filter until you get good results.
I think you're right, skipping points where the elevation is greater than the distance change is probably the way to filter it.
If I make it so we can adjust the limits on the distance change and elevation change we can probably fine tune it so it ignores mostly redundant data that contains variations on the same location.
I might be wrong, but it looks like BaseCamp might be rounding off the lat/longs before they compare them for distance. If you're looking for matches that would increase the number you'd find pretty quickly the more you rounded them. I might try that too.