If Naughty Dog never signed on to the company, there would be no Crash Bandicoot but they would make Al O. Saurus and Dinestein, a side-scrolling video game based on time travel and scientists genetically merged with dinosaurs, (a spoof on Back to the Future and Jurassic Park).
The prototype version of the game contains several (very buggy) removed levels, but also some other changes. Most notably, Ripper Roo was originally located at the end of the first island, along with "Up The Creek". (This would explain his rather awkward placing in the final game, just two levels into the second island.) The fight is also somewhat harder, and his laugh is slightly lower-pitched. There were also "POW!" crates, which don't kill you (oddly enough), but make a pretty explosion when broken. A precursor to Nitro Crates, perhaps?
Pinstripe was originally named Pinstripell Potorott.
Originally, "Sunset Vista" would have been EVEN HARDER and would have become even more of a Marathon Level, with an entire section at the end featuring things like rotating flame platforms. Thankfully, Naughty Dog had the good sense to cut this out of the final version and just end the stage where it began.
The bridge levels were also much more difficult, with crates floating in the void to the sides of the bridge, and the planks that collapse immediately being distinguishable from the planks with a delayed collapse only by a very slight color difference (in the final release, these planks are noticeably broken).
The original level order was drastically different overall. For instance, Boulders/Hog Wild were switched around as were Cortex Power/Heavy Machinery, Jaws of Darkness was originally on the second island just after Sunset Vista, Road to Nowhere immediately precluded The High Road, and Fumbling in the Dark was not a hidden (and, more importantly, optional) level, but instead was the penultimate level (just before the notorious Stormy Ascent).
Tiny Tiger and the Komodo Brothers were also designed to put into this game (hence their cameo in the prototype intro above), however they were omitted and spared for Crash Bandicoot 2: Cortex Strikes Back.
Aku Aku was a sprite in very early stages of development and Crash collected actual fruit and a Yin Yang Yuk item instead of the fictional Wumpa fruit.
As seen in an E3 build, "Whole Hog" originally became much more complex towards the end of the stage, with tribesmen hiding behind walls and boomerangs spinning through the air being thrown into the mix of obstacles to avoid (seen here). They were cut from the final game and replaced with more of the same obstacles used throughout the rest of the stage.