Not really an avid comic reader so I don't think I am your audience... but I can see the advantages of both. Personally if I am reading a story online I like to be able to open everything at once, then for turning the page I can simply close the tab. With comics though I guess the story progress is too fast, and would also involve opening dozens of tabs, as such I think I prefer the 2nd link of yours, which has the faded sections as you click through. Comic layout I guess can be a little complex wondering what pane is next, so it's nice to be led through it more.
Also while I agree having animated parts of the comic (ie characters, or panes flying in like some Powerpoint presentation) would not be good. The last section I think could have benefited from a more fluid zoom out motion (fading out the un-needed text).
How were you planning on implementing the 1 & 1/3rd page portion of the protests?
