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Mr Joe wrote:
Av mode can sometimes induce a flicker effect when assembling the time-lapse. This can be reduced in some software packages. Another option to look up for day/night transitions is called bulb ramping. This can be done with a Promote remote, or Magic Lantern firmware. Another option is to manually adjust the images -- here's a LRTimelapse video that explains how to do ramping without an external device: http://vimeo.com/57265142
Manual exposure doesn't prevent flicker, contrary to popular belief. Aim your camera at a white, constantly lit wall, and take a 1000 frame sequence and check for yourself. Even with the meter out of the equation, at any aperture other than wide open, the blades have certain tolerance and will not expose evenly. And in most cases you're not shooting a white, evenly lit wall, which will add to flicker (moving clouds, etc).
Bramping has the same problem like any settings adjustment - it requires two anchor points per adjustment, and that adds up pretty quickly. Doing a gradual ramp with Av (esp. if you use centerweighed metering and not matrix) is oh so much easier in most cases.
Like in most things, manual gives you the most control but you'll pay for it with time in post processing. I calculate about 1h per 1s of final movie, and Manual mode has the potential to blow it beyond that.