The year this came out it was my pick for best Anime of the Year, and is one of the only more Modern Anime to make it into my top ten of all time (At Number ten).
Despite a kind of plodding pace for the third quarter of the anime, everything else was an absolute wonder. I'd put the climax as one of the greatest final fates in all of anime.
I'm agree with you about the plodding, the anime could easily jump from episode 12 to the last 3 episodes, however the "filler" episodes are still fun to watch even though they don't contribute too much to the main plot.
I feel the ending as a bittersweet experience but also a necessary one for both Hyakkimaru and Dororo. I would like to see something else about this anime but considering there's a big chance to mess the original experience, it better keeps this way.