My main issue with f.lux (and the reason I don't use it) is that you can't configure it to wait until a certain time to start with the transition. When I go to bed at 11 pm, I would like f.lux to start its one hour transition at 9 pm so that I don't see that much cold light the last two hours before sleep. And in the morning it should start directly with the settings for the day, without any transition.
Tying it to sunrise/sunset is what makes it useless. In winter it starts the transition at 4 pm while I'm still working. The amount of daylight I get in winter is already low enough, using f.lux would make the winter depression even worse. I could of course trick it by settings the location to place in the Southern hemisphere, but that won't help me during spring and fall...
I didn't set it to be in the Southern Hemisphere but just moved it further West. I never notice the transition from warm-to-cold anyway (not an early riser) and it delayed the cold-to-warm transition by 2 hours.
Similar issue here. I love it but it starts too early and clicking the "turn off for a hour" setting all the time was just a pain. I like that it initially tries to auto-tune itself, but I'd enjoy it even more if it had a customizable schedule.
And this might defeat the purpose, but if I could configure it to know what Spaces it was in in OS X, I could still design and not have to turn it off manually for just that one Space with the browser window in it, where knowing the actual colors is important.