About the Dr Valentine being "not a real life form" business… I think there had been misunderstanding. What I was saying was that I had the following idea to fix the plothole of the first movie's neutral NIMH being apparently run by an evil mad scientist:
This idea was that Dr Valentine was meant as a
subversion of the "Obviously Evil Mad Scientist" cliché - he
looks like the guy you think would be the bad guy in a comic or a cartoon, but he's actually benevolent, as well as empathic towards his test subjects, as demonstrated when he pats a young Martin's head in the flashback. He just happens to look weird. Note that the only people from whom we are told that he's evil are the Lost Mice (and Jenny), who are naturally inclined to dislike him, since they're the one being tested on (and that's nothing inconsistent compared to the first movie, where Nicodemus similarly considered the animals to be "tortured").
My
second idea, following this one, would have explained why the NIMH laboratory suddenly looked like Dracula's castle. It was that another trope, the Fisher King Land trope (read about here:
http://tvtropes.org/pmwiki/pmwiki.php/Main/FisherKing), was into play here: when benevolent-Dr-Valentine was in charge (during the events of the first movie), NIMH looked fine. But when Evil!Martin took over, NIMH turned dark to reflect its new master's personality, in accordance with the trope. It's a slightly unrealistic note compared to the mostly magicless world in which the movies appear to be set, but first, it's not totally unprecedented magically speaking since we have the Stone, and second, at least it
is an explanation for the apparent plothole that fixes the continuity.
Oh, and I have a
third idea to explain the "dumpster expedition" that seems to be contradicting Nicodemus's philosophy: the fact that Jenner was considered a serious threat by Nicodemus in the first movie suggests that he was not alone. He had allies within the rat community, not quite as ruthless as him, and who never took part in Jenner's evil doing, but who still shared Jenner's opinion that "borrowing" stuff from humans was the right thing to do if they wanted to preserve their society. Especially with Nicodemus gone, the two factions probably had to compromise when they finally arrived to Thorn Valley.
It could something like this: the "pro-Jenner" wanted to keep taking human stuff to Thorn Valley to make life easier. The "pro-Nicodemus" argued that it was
wrong to steal, and the "pro-Jenner" (seeing how everybody knew Jenner had turned insane and evil in the end, which probably drew some allies away, making the "pro-Nicodemus" into the majority), probably couldn't totally reject that. But they said: "fine, fine, stealing is evil, but we can pick things in the trash, right ?". Justin, Mr Ages, and generally all those who had the moral clarity required to understand what you have all argued above (about how that wouldn't be right
either), tried to explain to the rats all of this, but most of them wouldn't understand the subtle morality at play, and said that the "pro-Jenner" had a fair point. The "pro-Nicodemus" didn't want that, but they didn't want a civil war with the remnant pro-Jenners either, so they let it be for the moment.