I actually think both the manga and the anime have lackluster last story arcs. The anime one is just plain horrible, an exemplary case of the "anime caught up with the manga" syndrome. So the anime creators had to make up a whole arc and they ended up with the incredibly awful Shimabara one.
The manga on the other hand, clearly meant to tie up the loose endings in the story. Most prominently the origin of the X shaped scar. It starts out very awesomely with the past chapters but the end battles and the 'Sanosuke's family' story left a lot to be desired as far as I'm concerned. I actually think Watsuki sensei grew tired of the series and wanted to pursue other projects.
I didn't like the change in drawing style either. It really reached a high point during the (equally sublime) Kyoto arc of the manga. Actually I guess that's my opinion on the entire story, both in art and storytelling the manga reached incredible heights during the Kyoto arc but the parts before and after it couldn't match it.
Which doesn't mean I look down on it, it's pretty much the best samurai fighting manga I have ever read and I gladly bought every volume. It just leaves me with that feeling that it could have been one of the best manga ever but just fell short in the end.