This is the same set of images, processed with a1ex's Deflicker program at default settings. I honestly can't say I gained a lot from the hours I spent in LRTimelapse. This did a remarkable job! I will play with it a bit and see if I can improve the product.
https://www.dropbox.com/s/gh1sr25u3wirpos/Deflicker.mp4
Well... after watching, I'd say the script didn't work :P
I have to add some more options - like adjusting percentile (something like 75% would have metered on the sky) or by cropping the image (so it will just meter the top-right area and pretty much ignore the water).
But overall it's a step in the right direction.
There was a fair bit of flicker left in the LRTimelapse version of the same RAW set. I spent hours trying to remove it. It did do a better job, but I don't think the extra time it took paid dividends.
The idea of selecting the sky is good, except that in this particular instance, I metered at the end for the city itself. I wanted to draw the attention away from the sky and down to the city as it came to life. I was able to easily do that in LRTimelapse and that part worked great!