It was probably because of low resources at that moment. The primary deciding factor is cost. Due to the size of the project with hundreds of episodes it is too expensive to produce high quality animation throughout. While it is correct that different animation houses and directors handle different episodes, they do not get the freedom to modify the animation style. The primary animation house, in this case Pierrot, manages the series "bible", a vast collection of characters and their gear and emotions and locations used throughout the show. This bible is what all episodes are based on and all animators, regardless of the shop they work for, follows this bible.
Of note, the factors that define the quality of the animation are the time allowed for the development of the key frames and the number of "tweens" that are commissioned. Key frames are like a storyboard. They set the baseline for the progression through the episode. The tweens, or inbetweens, are the frames that fill in the motion between the key frames. The more there are, the smoother the animation is.
