Screwed by the Network: The series was placed up against Pokémon in its prime and got crushed. After three episodes, rather than given a different timeslot, the series was outright pulled from the schedule. Over a year later, the remaining episodes were burned off - completely coincidentally in the months leading up to the release of the first movie.
What Could Have Been: The original concept was to adapt the first 26 issues of the Stan Lee and Steve Ditko comics. (The series was put into production for contractual reasons, per Will Meugniot, and doing the first 26 issues would've been a low-budget way to fulfill that requirement.) However, those plans came to a halt when Marvel sold the film and animation rights for Spider-Man to Sony Pictures, and hence Saban was unable to use the "actual" Spider-Man. Marvel eventually sent Saban a list of stuff they wanted them to use, including the symbiotes, Counter-Earth, John Jameson, etc., explaining the weird mish-mash of ideas and characters the show had. Meugniot then came up with a story treatment that included Spider-Man meeting the Counter Earth version of Peter Parker, who would have been revealed to be his world's version of Venom (as his Uncle Ben had never died, thus meaning Peter never gained the moral fortitude necessary to resist the symbiote). Marvel ordered this plot thread nixed because they felt it would be too similar to the disaster that was The Clone Saga.
One of the proposed plans for the series was to adapt Spider-Man 2099, but it was felt that Batman Beyond (then also in the works) covered that territory well.
A possible script for "Destiny Unleashed Part 2" can be seen here.
Also this website lists summaries for unproduced episodes and other ideas that reveal the following:
Spiderman encountering Counter Earth versions of Mary Jane and Black Cat.
Lord Tyger defecting from the Knights of Wundagor to form a goverment in order to unite humans and beastials together.