Well, you see, there are a few possibilities in making a new boss.

1) You can make an animation which will hurt you if you touch it. You must destroy a trigger crate to open the 'door' to the ending. Just evade it all the time... Could be quite boring to make, but it works.
2) Have an original boss, put it behind some layer3 stuff and shoot it with Seekers, ElectroBlasters, Bouncers, etc.
3) Be creative! Respawning baddies could also make good bosses, if you do it right.