Jeremy may be dumb for a corvid, but he most definitely has their universal attraction to sparklies.
When I was a kid, I always thought the weird images in the "our world began changing" sequence were supposed to be pain-induced hallucinations the rats were experiencing—just abstract nightmare images with no rhyme or reason. It was only after not having seen the movie for several years—and learning more about biology in the meantime—that I realized the twisty ladder-like structures were supposed to be DNA strands being disrupted, mutated...and as they changed, so did the way the rats viewed their world.
If the process the rats went through slows the aging process, why does Nicodemus (who was presumably the same age as the others when NIMH took him) look like he's about a hundred years old? Magic (or psychic powers, or whatever) appears to be physically taxing, judging by Mrs. Brisby's exhaustion after using the amulet, and he seems to use it almost constantly.
Why are you assuming that Nicodemus was the same age as other rats like Jenner? We never really see all of the rats/mice that were experimented on, and seeing as the animals were all shown being gathered from the streets at random there's no reason to assume they'd all just happen to be the same age. Therefore, it's very possible that Nicodemus was already a fairly old rat when he was originally captured, who managed to then reach years that'd be considered absolutely ancient or unheard of for a rat due to the experiments.
Some clips in this wiki describe the Great Owl as thematically a dragon. It makes sense; a giant flying beast that's both very dangerous and very wise in old age. Then I thought about the cobwebbing stuck to his wings and back. It just hit me, the webs are meant to make his normally feathered wings look like a western dragon's leathery wings.
Remember how terrifying the scene is when Mrs. Brisby tries to drug Dragon? Now imagine it from her perspective: the two she knows have done it have enhanced intelligence over her, but Mr. Ages broke a leg trying it, and Jonathan, her beloved husband, died in the attempt. She's just a mouse... oh, and one whose failure would mean a horrible death for her son, while orphaning her remaining children.
NIMH is a real world organization.
Not just that, but what happened to the rats and mice was based on real-life experiments. They were controversial, but they existed.
More sad than horror, but Jeremy's "Miss Right" is no where to be found in the sequel, nor does she get so much as a mentioning, suggesting the two may no longer be together. She acted as Jeremy's one Bone Throwing in the first film, so it comes off a little saddening for the poor crow.
Why was Jenner so determined to keep the rats from leaving anyway? You could argue that he desperately wanted to rule, but he could've ruled somewhere else too, and he knew NIMH was coming and would likely take him back to a life of imprisonment or death.
The reason Jenner didn't want to leave is because he's strongly against "The Plan" ( the rats leaving the rosebush, abandoning the lifestyle and technology they made there and moving to Thorn Valley). He even killed Nicodemus, thinking it would put a permanent stop to "The Plan." Additionally, he didn't know about NIMH arriving to find them, as Mrs. Brisby was the first to hear about it, and is in denial about her warnings and tries to make her out as a hysterical liar. Add to that Jenner didn't come off as particularly stable a being.
Also, Jenner was willing to fight NIMH. If he had stolen the Stone, it isn't hard to imagine he would have won.
Jenner was many things, but cowardly was definitely not one of them.
He is evil, though, so the courage of his heart is corrupted.
See just below:
Jenner's plan was doomed from the beginning because he did not know enough. First, living in the Rosebush longer was not only immoral (which he knew and didn't care about), but also impossible since N.I.M.H. agents were coming soon (and that he did not know). Later, he wants to get the Stone. But all he knows is that it's a magical stone with telekinetic powers. He doesn't know about the "courage of the heart".
The male characters who play a significant role in Mrs. Brisby's ordeal in the film (save for Mr. Ages and Nicodemus) have names starting with "J". Jonathan, her husband. Jeremy the crow. Justin the guard captain. Jenner the Big Bad.