Artistic License - Biology: Apart from the fact that trees don't have a nervous system and can't feel pain, the bark is made of dead cells anyway. Zak carving on it would be no more painful than trimming your fingernails.
Batty's size is rather inconsistent. He's definitely a fruit bat. But why is he only slightly taller than the fairies/Zak, who seem to be only a few inches tall at best? Flying Foxes are the largest bats in the world. With wingspans up to six feet wide. Even if you take into account possible stunted growth that's small.
Furthermore, he says his "radar's all shut up", but fruit bats can't echolocate.
The sequel is even worse - he goes from a few inches taller than the faries, to about the size of a baby wombat, to big enough to carry a human child. And back again.
Bittersweet Ending: Zak has to leave the fairies and go back to his own people, and it's implied he and Crysta will never see each other again. But he leaves with a new-found respect for what he once thoughtlessly destroyed, and tells his friends that "things have gotta change."
Body Horror: Hexxus gets a tree grown out of him. Twice. The second time is much more graphic. Considering the roots burst out of his chest and fuse him into the trunk, it's got to hurt.
Broken Aesop: Averted - at first you're concerned that the movie is going to tell you that the fairies can take care of it. But Magi Lune is very explicit that with damage this extreme, there's very little she can do to fix it. Zak tells his friends that things have got to change.
In the sequel it's truly broken - a forest fire burns down a large part of the rainforest. The fairies set to work fixing it, and by the time the heroes return triumphant, things are almost back to normal.
For all the times the first movie tries to show nature as beautiful and humans as destructive, the true villain of the film wasn't the humans, or even something created by them, but a living being who's pollutiing the forest so he can eat. Life is literally toxic to him, and pollution is his only sustenance. So basically, in a movie about how wonderful nature is, they made the bad guy a natural being whose nature is to feed on nature itself.
Clipped Wing Angel: Hexxus unveiling his stronger form doesn't help him much. Before he can even unleash his destruction, Crysta and the other fairies infect him with plant growth and seal him in another magical tree.
Cross-Cultural Handshake: In this case, Zak ends up introducing Crysta and Pip to shaking hands as a greeting; just seeing him extend his arm towards them, they do the same without even attempting to grasp his hand or arm back.
Crowd Song/That Reminds Me of a Song scene: If you'd like to see a bunch of magical beings dance to "Land of a Thousand Dances" for no reason at all, have we got a movie for you!
Dark-Skinned Blonde: Zak has noticeably darker skin than most of the fairies. Still, not so dark that it can't be a result of plenty of beach time; this is Australia.
Also, his hair could be dyed. Didn't you notice how dark his eyebrows are?
Fanservice: Crysta's outfit, if you're into that. Or Pip's, for that matter.
Fantastic Racism: Batty hates humans in both movies, without exception. Really hates them - he'd like to see them dead and sees them as monsters without feelings. Admittedly he has a damn good reason...
Not too subtle? The lyrics include the word "horny" — and it's not the "having or feeling like horns" definition either (though that original definition isn't used much — and this isTim Curry we're talking about).
What's odd is that in the scene of Hexxus sucking the oil from the machine when he first comes to life, the censors found nothing objectionable about him describing the oil he was consuming as "mother's milk" (to be fair, the "mother's milk" line was almost cut, but either the censors forgot or the writers fought to keep it, in exchange for having "Toxic Love"'s more sexual lyrics removed).
There's a different moment that may or may not be this trope: When Crysta tells Zak "I want to learn magic like yours" (a line which in itself sounds vaguely like... something else), he leads her to a flower, they both crawl beneath the petals... and it turns out that Zak's only showing her a lit match.
Healing Hands: Done by Zak to Crysta after Crysta accidentally touches his match and burns her hand.
Humans Are Cthulhu: Apparently all they do is create pain and pollution and destruction. But they're not all bad, because they also have boom boxes!
Humongous Mecha: The Leveler. It's a bulldozer, a tank, a tractor, and an automated factory all in one. It has two huge arms with giant claws for hands, chainsaws on its "elbows", and a "mouth" with backwards-facing "teeth" that pull unfortunate trees inside it, all topped off with a control room that looks like a single wide cyclopes-like eye. Basically, take Gigan and turn him into a vehicle.
Jerk with a Heart of Gold: Pips. He's a tough, badass fairy that hangs out with a group of biker fairies that very openly expresses his dislike of Zak multiple times, but he's mostly concerned about Crysta's safety and the survival of Ferngully. Near the end of the movie, he ends up saving Zak from falling to his death and helps him get inside the Leveller.
Lyrical Dissonance: "Batty Rap." Justified because Batty is, well, pretty much insane from the humans' experiments on him.
Made of Evil: Hexxus is the semi-incorporeal manifestation of destruction and pollution that has to be sealed in a tree to be contained. He wants to turn the world into a polluted wasteland specifically because he lives off it.
Mentor Occupational Hazard: Apparently whatever Magi Lune does requires that she die so her protege can take on her power. Why this is necessary at all is never explained.
Missing Mom: Crysta's mother is never seen nor mentioned.
The Name Is Bond, James Bond: When Batty introduces himself to the fairies, he explains that "they used to call me Batty. Batty Koda." That's a cute name, though!
Well, it's possible he was a bit strange before being captured, "Batty" is a nickname, and his name is simply "Koda."
Nothing Is Scarier: What did those scientists do to Batty? We get a few unpleasantNoodle Implements in the full version of his rap, but that's about it. Then again, since there are two wires sticking out his head that short-circuit his thought processes when they touch, it's probably better if we don't know.
The Obi-Wan: Magi Lune, though what she does and why Crysta is studying under her isn't really established. Nor is it established why she dies.
Off Model: As said in Animation Bump above, the first movie was done by a number of animation studios in America, Europe and Asia. For FernGully 2, however, only Wang was kept around, though Stardust Pictures was also used.
One-Winged Angel: After Hexxus' power source from human pollution is disconnected his smoke form dissipitates, and it momentarily seems like he's defeated. Then he harnasses his own power and transforms into a giant, black, cloacked skeleton made out of fire and tar. It's hinted to be his real form, as it's glimpsed earlier in the film during his Villain Song.
Running Gag: Batty Koda's consistent collision with trees (and anything) is a major running gag, and it even continues into the sequel.
Scenery Porn: The very colorful, lush environments are actually based off of what the filmmaker and a group of animators saw during their trip to the Australian rainforests and are arguably the most researched part of the movie. For example, the scene where Zak talks about life in the city seems to exist for the sole purpose of showing off the beautiful glowing mushrooms growing on the trees.
Screams Like a Little Girl: A frightened Batty does this in front of Pips' face making him jump back, after Pips teases him by telling him he loves his haircut.
Sealed Evil in a Can: The villain Hexxus, who for ages was sealed into a tree, and was released when the tree was cut down.
Skyward Scream: The mother kangaroo in the sequel, after her baby is stolen.
Soundtrack Dissonance: Or soundtrack flip-floppery, anyway. In the sequel, Batty flips from singing about how they'll most certainly get home if they don't give up hope, to hopelessly informing the other animals that they're all bound for the same fate he suffered before the first movie, and then some.
Space Whale Aesop: "Save the wild places in the world, because that's where the Fairies live." Well, if it works, that's good with me.
In the sequel, the moral is still to save the rainforest, even though we see several times the fairies can do to one their own. The moral of the story to him is "Don't save the rainforest, the fairies have it under control."
"Don't cut down trees or you may unleash an avatar of death that will destroy the world."
This Is Gonna Suck: Batty Koda, during a scene in which Hexxus nearly crushes both him and Zak with debris.
Batty:(watching a headlight falling towards him) Oh, this is gonna hurt...
Too Dumb to Live: The villains of the sequel, who could have easily stopped the truck they were driving and kicked the heroine off of it, but instead elected to murder her by decoupling their trailer with her on it.
This is Truth in Television. Because fruit bats are just so massive, they have a lot of excess inertia when it does come time to stop, resulting in rather hard landings. That said, they probably don't land face-first into the trunk.