- The Blue Orb doesn't represent any sin, since it only gives you meat.
- The Red Crystal represents Gluttony, because it turns into the giant profasu - an enemy from the second Era. The Era's antagonists? King and Queen Bee, who ate all the plants.
- The Blue Streaked Crystal represents Envy, since it turns into the Jellyfish, the weakest and the first enemy in the game.
- The Porus Purple Crystal represents Pride, since it turns into the Birdman swordsman, a swordsman belonging to a very vain, racist species.
- The Moss Green Crystal represents Wrath, since it turns into the Giant Zinichtys... and it's damn malevolent lunging at you.
- The White Pearl represents Sloth, since it turns into a Child Ikustega.
However, that leaves only the Spiked one (with the Giant Prosauro) and the Yellow one (Debustega) and Lust and Greed. I suspect that the Debustega is Lust, though.
Consider this - aside from being a humongous delusional amoeba with heavy Freudian overtones, there is literally nothing that makes Bolbox a bad guy. Hell, when he introduces himself to you, he is being actually pretty softspoken
and not threatening to kill you like any other villains do. And, if the endings that you get if you join one of the bosses' side are any indication, humans still appear. Not only that, Bolbox seems to be quite a neat guy, sharing his crystals with his allies, who either got the short end of the stick (Tyrasaurs and the Queen Bee) or were ostracized by their family (Cro-Maine).Oh, and, again, aside from being a Freudian huge amoeba, he doesn't seem to be an unsuitable suitor to Gaia. If that doesn't make him a Designated Villain, then he is not so different at best.
After their fortress crashes, Bird-Men realize just what egoistic dumbasses they were and fly off into space with the help of Martians. Hey, if you can fly into the meteor belt...
They're neutral.
What did you expect? They're literally a prehistoric animal trying only to survive.
Alongside that, the eras always end either when the player's defeated the highest life form or advanced further in their evolution. The player wants to be the strongest life form on the planet.
The player is out to become Gaia's consort in Eden. Gaia created the player, as Eve came from Adam's rib bone. The original PC-85 game ended with the exact opposite of the player and Gaia fusing into one being. That would also make the Sun the serpent of Eden, considering he gives the player the gift of intelligence as a reward for their hard work. Plus, the Martians caused the looked down upon enhancements in evolution, and the Bible canon states that God made everything in it's present state, with some churches even disavowing the theory of evolution altogether.
Also, since the player is Eve, that would make Bolbox Lilith, since he came before the player and is also trying to get into Eden with Gaia.
At the end of the PC-98 version, after Lucifer is defeated, we are told that "Physical evolution ends here" and that "with our minds and hearts as one, a new evolution will begin", and finally the entire earth becomes some kind of a glowing spaceship and moves away from the solar system. At the end of Advent Children, Sephiroth talks about how he plans to kill humanity and use the planet as a spaceship until he finds new worlds to seed. The entire EVO game was played from Genova and Sephiroth's point of view, where they consider themselves as fulfilling evolution/life to their full potential, by absorbing them, ruining the planet, and then spreading them to other solar systems. Lucifer in this case was evil just because she was a competitor from the same race as Genova.
