Load factors over 80% are bad because it means you charge not enough for your tickets.
Again, I can't disagree with you here. However, if you are flying out at 230 with a 60% load factor and returning at 600 with a 100% load factor, that flight is going to show up as having an 80% load factor on the manage routes page. I don't know how you manage prices, but if you have a life outside of AWS I assume you are managing route pairs and not each individual flight, otherwise it would be a full time job. Thus when load factors on a route pair are >80% you raise prices for all flights on that route pair. Otherwise, you'd have to dig pretty deep to find that 60/100% load factor flight because you should be raising the return flight prices. This is an inherent limitation of the current system and one of the benefits of the -40% pricing because when you have 60/100 load factors instead of 80/80 you end up not raising prices because of bad/limited data and system limitations. Not saying you are wrong, but you aren't doing yourself any favors with the current system if your outbound/return load factors have a huge delta.
For example, the first flight has 100% load factors on the ORD-DFW flight in GW2, but the route pair has a 92% load factor with 9 flights/day. I have 634 (1264/2) route pairs which is WAY easier to manage than the 23,000+ weekly flights (3000+ flights/day) I have, so I am basing my price changing decisions on 92% and not 100%. Hopefully the new revenue management features will make all of our lives much much easier when it comes to managing pricing AND has some built in features to help with load balancing to reduce standard deviations/variance.
I'm linking to this the revenue management thread for sami's reference.