How did Mario get abducted? Consider that a) Luigi had to be brought in remotely, b) E. Gadd was worried that the ghosts could escape the valley, not that they already had, and c) by the time you got to the last mansion, they still hadn't gotten all the local Toads into paintings. If it was just an early act by the main villain, that only raises the question of why he didn't deal with Luigi early either... and considering the first game, you can't say it was due to underestimating him.
The same reason he didn't turn Luigi into a painting immediately before the final battle. He probably wanted to taunt Luigi, metaphorically playing with his food. Or maybe he wanted to get stronger first, so that Luigi wouldn't be able to defeat him.
Also E. Gadd was concerned about the native ghosts of the valley escaping. The Boos were another matter entirely; he was surprised they were there at all.
Also, at one point Gadd mentions something along the lines of "I knew I should have come to you first." I figured that meant he went to Mario first, and while Mario is the bigger hero, he actually has less experience with full on hauntings, so the ghost probably got him then. Gadd not mentioning this later isn't all that odd considering he can't even remember how many Toad assistants he has.
That's a lot like how Mario was caught in the first game. He got to the Mansion first, and was grabbed. So I guess it makes sense.
The ghosts were originally made docile by the presence of the Dark Moon. By the end of the game, E. Gadd's claiming that they're being controlled by the main villain. So... what would they be without the moon or the villain? Purely chaotic? And isn't it a little too easy to say that the plot boils down to a battle to determine who gets to brainwash the population?
I look at it this way; the Dark Moon keeps the ghosts from going nuts. When King Boo destroyed it, they went insane and he used his powers to enslave them.
As far as the dark moon goes it's not so much brainwashing as it is therapy in radiant energy form. It keeps them from going insane but the greenies for example are still mischievous and getting into everything, it's just toned down to not dangers levels.
In between King Boo's capture and the Dark Moon's repair we see the Evershade ghosts turn on each other, a slammer is eating a greenie! That's what happens with no Dark Moon and no controller.
Why do the Boos look so much different than the other ghosts? In the previous game they were rendered with the same translucent/glowing effects and they even look that way in this game's artwork but in-game they're just... completely solid except when they're turning invisible.
Thats how they've looked in several other Mario games since then. Like 3D Land, for example.
It's also because the Boos are foreign to the setting of the game.
Boos have always looked and behaved differently than other ghosts. In the first game the Poltergust didn't pull them in (though it still weakened them), for example, and they could freely move between rooms and move about in light when no other ghost could. I think the implication is simply that Boos are a special, more powerful class of ghost.
If Boos gain power in numbers, why does E. Gadd keep them all together after their capture. Surely having 32 Boos all together could be dangerous in the future?
Which is to say nothing of the fifty Boos from the first game. E. Gadd isn't good at learning from his mistakes apparently.
Who's to say he hasn't already taken that into account?
Well, when you observe the Boos you captured, they don't seem to be trying particularly hard to escape. They even occasionally spin around lazily.
Boos for the most part are lazy, hovering jerks who'd rather hang around and scare people most of the time rather than cause any real trouble. King Boo just happens to be a psychotic lunatic among them who either convinces or scares them into obedience. Really, everything they do can be explained by either room for personal gain, satisfying a grudge, or fear/loyalty regarding King Boo.
Boos can be seen playing around in the Treacherous Mansion too, much like the other playful ghosts. Perhaps Boos have the mentality of (particularly cruel) children and just do whatever is fun?
Or the Boos could have released him. Since E. Gadd sold the painting at a garage sale, there would have been no one to stop them from letting him out, and we already know the Boos captured in the original game aren't the only ones under his command.
Already explained in-game, albeit not explicitly. You know how you use the Dark Light to extract keys, coins and Mario from paintings? Remember what was shown to be the culprit? Spirit Balls. Who gave Boos the ability to use them? King Boo, shown from his mastery of illusions to the point of warping reality. If he can turn things into paintings so easily, obviously he'll be aware how to reverse the process. Why didn't he break out right away? Why would he, when the guy who builds the things that can catch him is right there?When Gadd sold the painting, He gave King Boo the breathing room needed to escape without risk of immediate recapture. Nintendo doesn't have to draw us a map for everything, after all.
Why does E Gadd never guestion why there are fully functioning teleporters in abandoned mansions?
This is the Marioverse. Naturally occurring teleportation is so common, the only mystery is why the teleporters aren't pipe-shaped.
Because Gadd put them there. They activate with his strobe-technology, and they even have "Gadd" in their name. E Gadd put those teleporters up himself in the mansions to facilitate getting around before the Dark Moon shattered.
For the majority of the game, the Polterpup is on the loose, and Luigi's attempts to catch the ghost result in the Polterpup escaping before it can be put in the vault. The Polterpup also doubles as the game's Extra Life mechanic; if Luigi dies while carrying a golden bone, the Polterpup will come in, take the bone, and revive Luigi. Since the Polterpup is never caught, it makes sense that the Polterpup is always there to revive Luigi... until Treacherous Mansion, wherein the Polterpup is finally caught for good at the end of the first mission and isn't released until the Dark Moon is reassembled at the end of the game. Yet, dying on the second, third, and fifth missions while carrying a golden bone still shows the cutscene of the Polterpup taking the bone and reviving Luigi. While it's not out of the question that there are multiple Polterpups, as there are more in the ScareScraper, the game does seem to imply that there's only one Polterpup in the main story. So... how can the Polterpup still be there to revive Luigi when it's trapped in the vault for the last few missions?
E. Gadd let him out to help Luigi. Puts him right back in afterwards.
That explanation is a bit of a Voodoo Shark. How does E. Gadd know that the Polterpup will revive Luigi? How does he know when to release the Polterpup? How does he release the Polterpup without releasing all the other ghosts in the vault? How does he put the Polterpup back in the vault? Why would the Polterpup let itself be caught again when it seems much happier running free?
You said it yourself: more than one Polterpup. Perhaps the one they catch is the same as the one in the actual missions earlier, but the extra life Polterpups are just random ones who spotted Luigi had a treat on him.
Don't forget the Polterpup can escape from Gadd's vault as it pleases as we've seen in the main story. It only stays at the end because it wants too. It's likely it's just hanging around just out of sight looking for a playmate and possibly tracking Luigi when he finds the bone. And then when Luigi gets knocked out, it's got a perfect chance to snatch the bone without the risk of getting captured. And still being a Ghost Dog thanks him which bring him back (it's still a dog, afterall). Also, that's why the Pup doesn't show up when Luigi doesn't have the bone, it can't/won't find him.
In the level "Stop the Knightmare," where did the possessor get a suit of armor that big?
It didn't, notice how some of the items that possessors take over grow when they get possessed? The possessor just found a regular suit of armor and when it was possessed it grew to an enormous size.
Also, the whole fight takes place inside an illusion. It's no different than King Boo making spike balls rain down.
This may not be a good question, but it just bugs me. Why did the ghost have pupils? Sure, they lost them when the Dark Moon broke, but in the original Luigi's Mansion, none of the ghosts had pupils either, and the Dark Moon was never mentioned.
My guess is the Dark Moon gave them pupils. In the first game, the Dark Moon wasn't there, so they didn't have pupils.
In the first game, the ghosts you fought were all fake. Apart from the Boos and the Portrait Ghosts, they were all paintings brought to life by the real ghost who created them. All of the ghosts in this game are real, and the presence or absence of pupils functions as a visual cue as to whether or not they are being affected by the Dark Moon. Granted, it was never made clear exactly what the Dark Moon does to the ghosts, and it doesn't explain why the Portrait Ghosts didn't have pupils either, or why in that game ghosts retained the form and identity of their living selves while in this one dying causes you to turn into one of several types of ghost, but the point is that the mooks in the first game were all fakes, and the mooks in this game weren't, and that's what's important.
Why, in the end cutscene, does Gadd have a button to release the Boos? I mean, why in the name of Hylia (yes, I realize it's the wrong series) does he think that it would be a good idea to release the Boos that have caused so much trouble for him and Luigi?
What if something important got stuck in there? Or what if they needed the help of the Boos to fight a bigger threat? Or what if they wanted to make another sequel?
There's a number of claims that King Boo has been controlling the ghosts. This likely applies to the Boos themselves. So once the threat of King Boo's presence (and more specifically, that crown) was gone, Gadd felt it was safe enough to let the Boos go.
Why does King Boo seem to think that he's won just by intercepting the Pixelator stream and dragging Luigi back into his dimension? Even if Luigi loses the fight, King Boo's plan for world conquest still hinges on the Dark Moon being shattered so that he can control all the ghosts, yet the final piece still managed to make it back to the Bunker, meaning E. Gadd now has them all and could have easily pieced it back together. (And stemming from that, why doesn't E. Gadd actually do just that until after Luigi defeats King Boo?)
King Boo likely figured he could just break the Dark Moon again, and given that everyone would expect that a second time and the strength of the possessors it's likely King Boo would have been ultimately defeated when he tried. Still, game over for Luigi if he at least wins there, and that prospect was probably made King Boo happy enough not to stop and consider just how far he had been set back.