Early Footage

It's probably just odd compression or something, but the area seems very blue in the screenshot, while the final is green. Marco is missing the empty energy gauge in his HUD, there isn't a Heavy Machine Gun in that area in the final, and the giant eel always seems to have it's mouth closed when it enters the cave in the final.

Probably another compression error, as the colours seem to have blue and red tints, and the clouds seem less detailed. The missing prisoner and HUD with lack of energy gauge seem to be the only other differences.

There aren't any suicide bombers or mines when you're fighting the giant submarines, and of course, missing the energy gauge.

The crabs look more red than orange, but as I've said a million times, it's probably just a compression error. The HUDs are, once again, missing their energy gauges, and it looks like the battle with the two crabs took place elsewhere in the area, what with the background being different, along with there not be boxes there.

Once again, the colours are off, and the energy gauges are missing, but what's interesting is that there are four soldiers on the enemies' boat. In the final, there's only ever two people on the boat, with the second coming out after the first one chickens out and drowns himself. It's also worth noting how close together those four grenades are, despite there being only three visible soldiers who could've thrown them, and they would've had to get out and come to the other side at roughly the same time to get them that close.

This and the following are of the PlayStation 2 version, where for whatever reason, the images in the menus of the manual and the game are entirely different. Thanks to Galvatron for telling me and providing the images.

Arcade was relocated from Mission 1 to Mission 4.

And the same applies to Arcade Score.

Key Config became Controller Config.

And they reversed the confirm and cancel buttons. Wacky!