Although they all praise the performance of the voice-actors (especially Jimmy Olsen's VA), the production team has a very low opinion of "Superman's Pal", an episode of the third season focusing heavily on Jimmy Olsen.
They have a low opinion of "Little Big Head Man", which they felt tried and failed to recapture the success of the earlier Mxyzptlk episode.
Off Model: The animation team did this intentionally, removing the "S" shield from Superman's cape in order to save themselves from having to animate how the shield would look as the cape rippled and moved.
The original, much darker plans for "Little Girl Lost" involved Superman discovering that Darkseid was turning humans into Parademons, with heavy Nazi overtones for the transformation camps, and the episode ended in the midst of a large scale battle on Apokolips. The authors do like the finished episode, but were very disappointed with the heavy backtracking after they had already been given the go-ahead for the initial plot.
"Legacy" was intended to kick off a season's worth of episodes about Superman regaining the world's trust. However, a pushback and other projects (Batman Beyond) led to it being produced as the finale instead, while the theme of public distrust for metahumans became an underlying plot thread in Justice League.
Clancy Brown, who voices Lex Luthor, originally auditioned for the role of Superman.
Sherman Howard was considered for the role of Luthor, having previously played the character in "The Adventures of Superboy". According to Bruce Timm, Howard gave an impressive audition, and was nearly offered the role . . . until Clancy Brown walked in. Howard gave one-off performances as The Preserver and General Steppenwolf, and later voiced the Luthor-like Derek Powers in Batman Beyond.
Paul Dini and Bruce Timm originally wanted to use Kara Zor-El as Supergirl, but they were denied by DC Comics due to the then-current "Superman is the only survivor of Krypton" edict.