1:14 Maybe the water stage was intended to have some octopus midboss very early on, so they used energies to test the wavy pattern. It could have also been used for the scorpion enemy's tail.
8:20 It should be noted that the game loads up the wrong palette for this enemy. If they had included it, it would have probably been colored the same as the others and placed somewhere in-between them.
5:00 Fighting the ride armors could have been the coolest thing in the world. With the fact that it uses the sitting graphic when exploding, I think we could assume at one point very early on you could fight the ride armor. Or it was a testing thing for Vile X2.
I think the upside down enemies were meant as placeholders until devs decided whether or not to include enemies crawling on the ceiling. However, there aren't many areas such an enemy would have much purpose. If they went from upside down to right-side-up in a drop-down ambush, that might have been another tactic. I think the locust bots in the electromagnet area of the junkyard were initially planned to pull a midair switch and dart after you. Not a huge deal but... looking back actually that's one of those small touches which would have put more spiff in that stage.
My version of the X2 and X3 final release titles had "unused" characters and motions....Those two being the only examples, I miss being a part of, “the bleeding edge in technology”, culture.