Marigold Girl idolizes Queen Tara and asked her mom if she can be queen when she grows up. She does become the new queen. She's not given a name, but let's look closer: MARIgold Girl or Mary. Remember that in the Bible, Mary was chosen by God to help the world. Queen Tara chose Marigold Girl to continue helping their world.
The significance of the name "Mary"/"Mari" is a lot more personal than that, if you know the history of the author whose work Epic is based on: his daughter Mary Katherine died of a brain tumor shortly before this film was made.
Tara's choice in a pod represents first-time audience's expectations: Similar to Mub and Grub thinking she'll pick the biggest pod, the audience would think that MK is the next heir. And by exceeding their expectations by choosing a small pod, her choice in the Marigold girl was not the audience's first guess.
Why can we easily see flies but not the Leafmen? Why does Terra blur when lying still, but a fly doesn't? Because even though they are bigger, the Leafmen are moving faster than insects. Insect wings in motion become a blur to the human eye, but when a bee flies past MK its wings are beating very slowly, slower even than the hummingbirds' wings.
Boggans and their forces expressly represent rot and decay, but mushroom characters are heavily implied to be allied with the forest proper. Mushrooms being fungi that feed on decayed matter, they'd logically be Boggan-servants instead.
It's much more likely that the Boggans cause unnaturally fast decay at a rate that would cause complete destruction of the forest, while the "good" decomposers like the mushrooms cause decay at an ecologically-sustainable speed.
On a similar note, decay is actually a vital part of ecology, so portraying it as a force of evil is actually rather ignorant for an environmentalist film.
HEALTHY decay is a vital part of ecology. The level of destruction that Mandrake was aiming for was decay that was at an unnatural speed and rate. There's a balance that the Leafmen were aiming for by keeping it in check. Allowing Mandrake's influence to spread even an inch would have taken umpteenth square miles of forest.
Mushrooms aren't just about decay: many species are symbiotic with trees, extracting minerals that plants can't easily acquire from poor soil and exchanging them for a share of the sugars which trees send down to their roots. It's likely that the forest wouldn't even exist without the help of such fungi.
Mandrake says Tara heals what they destroy in the name of balance, and that his desire to destroy the forest is a reaction to his being unable to make any lasting impact on the forest. Instantly regrowing anything that dies and keeping the Boggans contained in a single "island of rot" amidst a massive forest does not seem particularly balanced. If the Boggans are meant to represent decay in general, keeping them separated is actually creating an imbalance in the forest: overgrowth. Although it doesn't excuse the destruction, Mandrake's frustration becomes somewhat understandable. However, if Boggans represent only unhealthy, dangerous decay, one can assume they are still around only because the Leafmen are unable or unwilling to destroy them entirely, and keeping them contained is the next best thing.
If it's really bothering you, it's also possible to interpret the Boggans as representative of invasive species of insect pests and plant pathogens, that don't actually belong in that particular forest at all.
Crows, bats, and star-nosed moles appear more or less OK with serving Boggans, even though the Boggans are destroying the ecosystem that these animals are a part of. How come there aren't any of them in the living forest? That's where they would rather live in real life.
There most likely are at least neutrally-aligned bats and moles living in the forest, but being more elusive than other forest creatures (bats being active only at night, and moles living almost entirely underground), they don't have much prominence outside their own ecological niches. The crows, on the other hand... Well, they are at least partially carrion eaters, so maybe a large number of them have simply run afoul of the Boggans?
Furthermore, every animal bigger than the Leafmen and Boggans appears to be non-sentient, so those employed by Mandrake probably have no say in the matter.
The fact that the Boggan leaders dress in the skins and skulls of the same animals they ride supports the notion that they are forcing their steeds into obedience, not cooperating with them.
Grackles, not crows. Look at the tails and listen to the calls.
If the fruit fly had a lifespan of a couple of minutes, how did he have enough time to get into the party and get a drink? Was he born there?
The thought of MK going off on her own. She's 17 years old, and in a vulnerable state of mind; who knows what could've happened if she actually left for good.
Odds are M.K. had Aunts and Uncles, or Grandparents that she would have gone to if she had left her Dad.
In the closing credits, we see a bullfrog skeleton. We only see Bufo, a bullfrog, in two scenes; in the last one, he insulted Mandrake's son Dagda, shortly after his death.
