Some other things that are different in the prototype version of The Revenge of Shinobi:

Many music tracks are missing. Tunes such as "Ninja Step" and "The Dark City" just aren't there. This means that which music is used on each round is usually different compared to the final version.

Some of the music sounds different in the prototype, most notably "Terrible Beat" and "Over the Bay".

The text intro sequence and the round demos are not featured in the prototype.

Once round 8's boss fight ends, the prototype goes back to round 1. There is no ending sequence in the prototype because of this.

Many of the sound effects are either different or not there at all in the proto. For example, Joe does not yell when using a ninjitsu technique.

Using the mijin technique counts as a ninjitsu attack in the prototype, whilst in the final, it doesn't.

The first boss recovers a lot faster from being hit in the prototype, making him considerably harder than in the final.

In the proto, the game over screen plays the level complete music, and does not have the evil laughter the final version features.