Most of the time, the cause of time lapse flicker can be attributed to the type of lens/camera combination. Here's why: on cameras with electronically controlled apertures (Canon DSLR e.g.) using an auto focus lens, the cameras default position aperture is wide open for best metering and then stops down at the moment the shutter is pressed. Say your lens is an f1.4 but you're shooting at f8. Every time a picture is taken, the camera closes the aperture for the split second of exposure. Over the course of a timelapse, the tolerance of opening and closing is not exact and creates the minute exposure variation known as flicker. The only way to avoid this with an auto focus lens is to shoot wide open, but of coursenthatnis rarely acceptable. Using a plugin to cure this will always yield inferior results.
The way to fix this is to use manual focus/manual aperture lenses like a Nikon AI or Zeiss ZF on a Canon (Zeiss ze poses the same problem as using canon AF) using an adapter. Then the aperture can be manually set and left in position for the duration of the shoot.
The second type of flicker comes from minute changes in exposure from cloud/sky variations. This is hard to fix, but usually not objectionable.
A third type of flicker, usually a problem for indoor timelapse or stop motion is tungsten light flicker from an unregulated power source. On professional stop motion shoots, we use voltage regulators to cure this.
(One poster mentioned progressive vs interlaced. This is not relevant to the discussion of how to remove flicker from timelapse footage as I would assume we're all working in an NLE like final cut to get away from dealing with interlacing. )
My advise: buy a couple of old manual lenses and an adapter and your problems will be solved.