There's a reason every series with several hundreds of episodes have to sacrifice quality
You're comparing the animation of a high budget short film to an episode in a long running series. Expecting movie quality episodes in a series like this is ridiculous, we're lucky to get any at all.
Also, the only reason the Chikara arc looked so good was because it was originally being produced as a movie, not episodes for the anime. Chikara was going to be 2012's movie, but they put it aside and decided to do Road to Ninja instead. So they took the leftover "Chikara" movie and turned it into 6 episodes.
