I think maybe there could be different missions in each level. Like you could take a path that leads to one villain, while the other path leads to another. Also thinking maybe the game could use more bosses that aren't fat.

Swinging Squirrel: Quick, evasive enemies that are hard to kill with physical moves. They also like to throw bombs that cause Exploding Damage.
Lizard Ninja: With long swords, they trade their piercing damage for an even stronger slash attack. They're also quite fast.
Hypo-Hornet: These creatures can cause poison, and have a piercing attack that drains HP.
Box Devil: They throw dynamite from behind a box. Weak HP, but high attack and defense. Fortunately not that fast.
Hugger: This cute little guy, like the hostages, is not an enemy, and you will be penalized for harming one. Huggers love to see the biggest, most huggable creatures around. If you sacrifice a Gordo Grande gem for them, you will get something really good.
Peggy Bob AKA Wolfman Stone: This Wile E. Coyote lookalike is an alternate boss of level one. Either defeating him or Thrump is required to move to level two. He takes much less hits to beat than Thrump, but is faster and comes equipped with plenty of status inflicting moves, as well as a Blind curing move.