I liked most of the new characters. They all fit well and skirted the line between entertaining and irritating, barring the Vigilantes, who were all absolutely awful.
Espella is the most important, probably, but I find myself struggling to remember her. She played the role well and I was never really annoyed by her, but she's not really much of a character. I don't know much about her likes, dislikes, or anything like that. I didn't really know what she DID in the town. She was functional, but not interesting.
Darklaw was the most fun to watch. The second I heard her name, I burst out laughing because DARKLAW. My god, that's the most fantastically obvious name for a villain/antagonist. (The reveal at the end actually makes it a tad brilliant, but still) Otherwise, she was fine, and made a very entertaining opponent in court. I actually found myself liking her younger self better, who only appeared for one cutscene.
I actually didn't notice until later, but she's actually a lot like Aura Blackquill, which is interesting to note. Did they like her so much that they decided to use her again in DD? I think the reason I never noticed was because Darklaw was more authoritative and was in charge of things outside her own plans, while Blackquill wasn't really in charge or anything, and only showed up when she needed to. I think Blackquill ultimately left a bigger impression, though. Darklaw's personality could probably have benefited from a few scenes with Espella.
I think Barnham was one of the better ones, his appearance only hampered by the fact that he barely factored in at all for the last part of the game. He was swept aside quickly and I kept waiting for him to return somehow, but ultimately he came off as wasted potential. Constantine was adorable. I was half-expecting him to have been an actual prosecutor, and for the stinger, he'd show up as Phoenix's opponent in regular court. I also expected him to have sort of a bigger turn, where he realizes that burning witches for just existing is kind of rude. That kind of happened, but not to the extend I was hoping.
From the witness side of things, I liked most of them. As I said before, they skirted the line between entertaining and irritating, but I found something to like in most of them.
However, the Vigilantes did NOT, and I will start with them because they were awful. The mob trial quickly lost its appeal to me the second "10 witness lineup" came onscreen, which, while visually impressive, was not something that was fun to play through. All the vigilantes were basically one-trick ponies with little character or entertaining qualities. Their designs were unappealing and generally lousy, and Wordsmith was one of them for absolutely no reason. Also, weird thing: the Head Vigilante always spoke with the female text voice, so I half-expected him to be another witch-in-hiding somehow. Ultimately, though, he was just like the rest of the vigilantes; terrible, boring, and pointless. I think literally 90% of them was window dressing. (If you wanted to know which one I hated most, I'd have to go with the tiny one because of the constant snot dribble. Ugh.)
On the side of witnesses I liked, I found Emeer Punchenbaug to be pretty great. I jokingly refer to him as "Layton and Wright's Greatest Foe" for singlehandedly turning the entire court back on them, and repeatedly screwing up peoples' plans. He was bemusing and slowly seeing how he'd fudged things up was a great pleasure. Some of the other witnesses were bemusing. The rest were just on that fine line between "meh" and "okay shut up now".
On the witches side of things, I liked both Kira and Greyerl. Both were presented as sympathetic characters, making the Witch Trials that much more threatening and immoral. Kira was probably more entertaining for her breakdowns and dark-side. They were also both plot-relevant, so that was nice. Greyerl was also pretty cool, and is probably the most sympathetic character in the game. She's very likable, even when you're against her, and I found myself hoping she didn't get torched.
Storyteller was certainly... there. He had a presence, and was important to the story, but I think he faded a tad too much into the background to be interesting. I think his main role was to explain everything to the audience, and just be cryptic and menacing otherwise. I think honestly 90% of everything he says is exposition, and the other 10% is "cryptic villain-sounding things". I particularly loved how he just casually brings up by the end "Oh I was dying of a rare disease" and then literally two seconds later he reveals there was a cure. Brilliant.
Oh and that brings me to the plot. Oh, the plot holes, the GLORIOUS, GLORIOUS plot holes. Plot holes large enough to drive a truck through! Plot holes so large and wide and totally expected from a Layton game. The first thing that comes to mind is the "hallucinogenic gas" thing that was borrowed from Diabolical Box, which was honestly the least of the plot-holey things. Honestly, I wouldn't have had a problem with most of these if the reveals hadn't all been crammed into the final few seconds of the game. There was no indication of the giant machines anywhere else throughout the game, and in spite of never seeing them, wouldn't someone at least HEAR them? In fact, it would probably be a lot better if there was strange, gear-grinding sounds throughout the whole game that nobody could explain; then BOOM, giant claw-hands! Would've made the reveal so much cleaner. (Also, Luke; took a crash course where? Do they just leave "How to pilot giant invisible claws" lying around the place?)
Honestly, I didn't expect them to go the "Magic isn't real" ending. I fully expected that it WAS another world, since that was basically the ONLY way to seal up the metric buttloads of plot holes. I even told my brother that there was no way that they COULD pull that.... And look how wrong I was. I don't know if the game would have been better if magic WAS real, but if nothing else, the twist did take me by surprise. (This twist also makes me think: either the Judge got SO fed up with his life that he agreed to be hypnotized, or that there's someone who looks EXACTLY LIKE HIM that's been hypnotized.)
On the side of twists I DID like, I actually liked the one with the Belltower reveal. It made a lot of sense... Until you wonder how nobody ever bumped into it or anything, but okay whatever, it looked cool.
Overall, I greatly enjoyed it. This was the game I bought the 3DS for, and it did not disappoint. Were there plot holes? OH GOD YES. Do I care? Not particularly. The game was still plenty enjoyable for the sheer awesomeness there.