Executive Meddling/Old Shame: According to this interview with Danny Wells, Nintendo was reluctant to do the Super Show from the start and had to be cajoled by DiC Entertainment to make it work. Nintendo finally agreed to license the series but wanted no more after production for its lone season ended. This may also explain why there have been no Western Animation adaptations of Super Mario Bros. since 1991. (the Saturday morning show Captain N and the New Super Mario World lasted a couple of years longer, regardless.)
Some of the live-action segments that aired alongside episodes of The Legend of Zelda were not restored when Shout! Factory released the series on DVD, one particular example being The Treasure of Sierra Brooklyn. Four other live-action segments that were not originally attached to episodes of "The Legend of Zelda" were not released on DVD either, as Shout! Factory either couldn't secure the rights to those segments or didn't get the proper masters for them
As this link states, the poorly-received 1990-91 Re ToolClub Mario disappeared into a black hole after it was taken off the air, and there are longstanding rumors that the master tapes were trashed. However, the Club Mario version of the episode "The Unzappables" is the one that's on iTunes, Netflix, and Amazon instead of the original version. Some attempts have been made to Keep Circulating the Tapes though.
The NCircle Entertainment series release cut out all of the live-action segments as well as the cartoon episode "On Her Majesty's Sewer Service."