I have nearly finished the project, there are some minor bumps left as I 
was not aware that the ships on the left side also move. The result can be 
seen 
here: https://www.dropbox.com/s/j97egbagvy6kiwh/lake_zurich_timelapse.mp4
There is still some more de-birding to do, and of course a soundtrack and 
so on...

But a time lapse video can be aligned with hugin.
Workflow (best do most of it on the command line):


   - Deflicker raw image stack with LRTimeLapse or similar
   - crop what your really really never will need away
   - render jpegs with some oversize in Lightroom
   - pto_gen to generate a file that contains all jpegs
   - cpfind --celeste --linearmatch
   - delete all CP's that are not in a designate area (script)
   - check if all images are connected (GUI)
   - run optimizer in GUI or autooptimizer (took only... a day or a half)
   - Hope for god results
   - delete CP's that are way off
      - the CP list is your friend!
      - sort by distance
      - select all "bad" CP's ie CP's that are on a moving object
      - whether you delete a single CP or many, the delay is approx. the 
      same.
   - reoptimze (took only 6.5hr)
   - output the now aligned image stack
   - ready for the video app

I wasted only some 2 days of computing time, but the final product is quite 
OK and the next will be better ;)

-- 
A list of frequently asked questions is available at: 
http://wiki.panotools.org/Hugin_FAQ
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