You'd think the Zombie Heroes would actually be called villains, since they work for Zomboss, and yet when you play as them, the plants are the villains. Remember that a hero is someone who is "admired or idealized for courage, outstanding achievements, or noble qualities." It's not a battle of Good vs. Evil, it's a battle of "Plant ideals" vs. "Zombie Ideals".
The Red Alert Limited-Time Mission (available as a promotion to the RED+ Charity) seems to have nothing to do with AIDS until you realize that zombies themselves are a walking, shambling virus and the Geranium plant (which is also conveniently a flower, much like Rose and most of the plants she uses) is used to Cure HIV-1.
During gameplay, Plant teammates face to the right while Zombie teammates face to the left, regardless of which side the player is playing. Now, in Plants vs. Zombies and its sequel, which direction did the plants and zombies (generally) face during gameplay?
The turn order mirrors the gameplay in both the original game and its sequel. Zombies play their units first (Zombies enter the lawn), Plants play both units and tricks (like placing a Peashooter or using a Iceberg Lettuce for example), then Zombies use their tricks (such as Gargantuar Prime, Wizard Zombie and Octo Zombie using their abilities on the plants you've placed down) before both sides attack.
Primeval Yeti's original description states that his lunchbox is just a solid block because he hasn't invented "opening things" yet. Yet, his Evolution ability clearly has him open his lunchbox to give the other zombies a buff. At first, this looks like blatant Gameplay and Story Segregation, but since he only does it when Evolved from another zombie, it allows him to do so because he evolves the method to open it!
The zombie mission "Everythings Coming Up Goats" ends with Rose hitting herself with the Goatify spell (thanks to Super Brainz mirror), this turning her into a goat. This means Rose has the magic to turn zombies AND plants (and presumably humans as well) into goats. Now, imagine if a zombie were to get their hands on her wand...
The zombies would need to know how the spell works, as Rose is a powerful sorceress and knows how to cast a Baleful Polymorph spell. And they probably do — Immorticia is the Zombies' resident sorceress and might be able to know how to cast it, much like the Wizard Zombies from the second game.