There was going to be a Spin-Off game called Saints Row: Money Shot/Saints Row: Drive-By, which would have been about an Ultor assassin named Cypher, which would have taken place between Saints Row 2 and The Third, and would have bridged a few gaps like closure for Dex, with Cypher assassinating him. The game was never made, and Money Shot was instead released as a standalone clothing and weapons pack (getting Money Shot would have allowed you to unlock the outfits).
Originally, you were going to unlock the Syndicate tower as a crib if you chose to spare it, and it's still presented as one. Also, the storyline changed many times during development, leading to many elements being dropped. Shaundi was originally going to get a big piece of Character Development and deal with survivor's guilt instead of going all Ax-Crazy, and Gat was going to be revealed as alive and well, and in need of rescue.
That second plot appears in Saints Row IV.
Averted with the Fart in a Jar which was originally cut. After revealing that it was one of those ideas that had been cut there was outcry that it should be Included. Volition listened and it was added to the game.
Originally, the gang specialists were going to be included as Homies. There is a TON of recorded dialogue for each of the gang specialists, especially Kirsten, the Decker's cyber-skating Shock Hammer wielding specialist.
Killbane was originally going to use a dirty bomb to destroy Stillwater, giving the player extra incentive to kill him. This was dropped alongside Shaundi's survivor's guilt story arc for being "too dark".
The Kill Killbane ending was supposed to be the original Canonical Ending for the game. The Expansion Pack, "Enter The Dominatrix" would've continued the storyline based on the idea that The Boss let Shaundi and Viola die in order to kill Killbane.
Despite the presumed implication of the ending, Enter the Dominatrix was to have Shaundi alive even though the bomb went off, and the internal names of some audio logs indicate they were originally meant for Viola, even though she too was supposed to be dead.