Hi Ben,
First thing to know is that WCS is not takign any action on power or channel assignments.
The access points basically start at max power and will lower their power if they hear about 3 surrounding APs at a loud level. This is how WLC achieves good coverage.
This means you can have 2 APs really overlapping on their coverage but that's usually not a problem if they are on different channels.
It also a misconception to think that on a map, all neighboring APs should be on different channels. Sometimes, APs are close on a map but far away from a signal perspective (obstacles). You have to take the load into account as well. If 2 APs are not loaded at all, it's ok for them to be on the same channel if that helps other APs somewhere else.
And don't forget as well that the real world is 3 dimensional. Meaning the WLC algorithm take into account above and below floors while you might not think about this point by looking at a WCS map.
So, although I agree that a very good site survey might give recommendations that are slightly more fine tuned than what the WLC would achieve, I think WLC does a better job than a humain assigning channels by looking at a map and not taking on-site measurements.
This said, I don't know how is your network :-) But I'm just raising the fact that the WLC algorithm takes much more factors than a human can without taking lots of on-site measurements.
Regards,
Nicolas