I'm writing this on 4-9-15, the night before Xenoblade comes out. I'm excited to play, although I'm also working to make sure advance expectations don't torpedo my gameplay experience.
Everything you said about difficulty sounds borderline ideal; I've always been good about adapting myself to whatever structure a game wants to impose on me, and it's rare for me to leave content on the table unless I feel actively antagonized by the design. (Side note: I know you didn't love The World Ends With You, and I don't think I've ever heard you talk about the Kingdom Hearts games, but I've always found their approaches to difficulty very rewarding; the ability to tune your game to precisely your preferred level of challenge, with extra benefits for pushing yourself to harder extremes, is very satisfying to me. There's a whole other conversation about how Square has used the games between KH 2 and the upcoming (presumably) 3 as laboratories for weird advancements in character development systems.)
|Not pictured: Bring Da Funk, Bring Da Noise
The act structure certainly makes sense to me, to the extent that any traditional narrative structure can work when mapped to 60-hour continuous narratives. (I've never really thought about that before, but there really isn't a direct parallel for that kind of extended storytelling, outside maybe a longer novel, in the Western artistic tradition. Nothing else is that long, without built-in episodic divisions.) Certainly, the rise of Telltale's episodic model (and before that, games like Alan Wake, that intentionally mimic the beats of TV shows, down to having "episode recaps" between gameplay portions) have codified that act structure. But they're not hard to see in older games; Chrono Trigger is broken into discrete chapters, while Final Fantasy VI slaps the player in the face with its split into two parts. Even games that aren't that overt can be broken down into changes in the party's objectives, and the overall tone. (Final Fantasy VII would be something like Act One: Midgar, Act Two: The Pursuit Of Sephiroth, etc.) I'll keep an eye out for them in Xenoblade when I start to play.
I look forward to seeing synthesis at work in Xenoblade; there's something very satisfying about feeling story and mechanics work hand-in-hand. (I wrote about how Bravely Default craps the bed in its last half when it abandons that synergy in one of the guestblogs I wrote for you, and there's an essay buriedsomewhere in my blog about the satisfaction I feel when Achievement systems act in harmony with gameplay and story.)
|The Walking Dead
To answer your specific questions:
1) Comedy in games is such a hideous, weird beast. There are very few games that manage it, and even fewer that can do it through gameplay, not through simply aping the comedic beats of movies or TV. (Super Meat Boy is a game with funny gameplay, for instance, as is Dark Souls (drink!), games where the levels and traps themselves act as jokes.) On the other hand, games like Super Time Force Ultra have legitimately funny dialogue, but it only rarely impacts the gameplay. (If I'm using your model correctly, that would be juxtaposition, right?) As for comedic mascots being funny.... I'm going to say never? I have vague positive feelings toward goofy little Chu-Chu in Xenogears, but that's about it. I can find the character charming (although that's rarely the case), but in general I don't think the majority of RPG designers and writers understand humor.
|Good RPG comedy sidekick
Oh, wait, does Morte from Planescape: Torment, count? I think he'd qualify, but that just underscores some issues with the difficulty of translating comedy from one culture to another, I think.
2) I don't have a problem with games using references as shorthand, as long as it doesn't lead to laziness. On the other hand, I'm not especially well-versed in Japanese culture (for instance, gasp, shock, fainting spell, I've never watched Evangelion and know it only through reputation/TV Tropes), so a lot of those references aren't going to land for me. In a way, that's nice, because it allows me to find originality in places it wasn't necessarily present, but it also means that shorthand won't work for me in a lot of Eastern RPGs. The Grand Theft Auto games, on the other hand, use it quite well (up to a point). As power fantasies, the game almost explicitly telling me, "Oh, we're doing Scarface, now," feels great. The Saints Row games take that even further, using musical cues and even references to the plots/styles of other games to communicate what the player's going to do next. They also don't fall into the trap of GTA IV, where Rockstar got high on its own supply, so to speak, and decided that they could tell a heartfelt tale of violence and redemption entirely through cues taken from other works. (It turns out that they really, really couldn't.)
Skipping over 3) because, shock, faint, someone get the smelling salts, I don't respond terribly strongly to Miyazaki and thus don't feel qualified to talk about his influence,
4) This one comes down entirely to the amount of player choice I'm given. There's something deeply unsatisfying about being locked into the role of a villain, forced to make the world darker and grimmer with every step, with no chance of redemption. (I turned Far Cry 3 off early on, both for unrelated reasons, and because I could see the outline of the story and wanted no part in it.) But give me a choice in how it plays out? Give me the option to be a knight or a knave? Well, a lot of times I'll still choose knight. But when I do decide to go for the Dark Side points, it feels like a narrative of my own design, and thus relieves me of the feeling of being trapped. Because Xenoblade is a JRPG, I'm guessing that won't be the case; true narrative choice is scant on the ground in games of its ilk. But I can remain hopeful! Of course, it seems just as likely that my characters will think they're doing something good, only to find out they've manipulated into evil, because that's how 99% of JRPG plots go. We'll see.
Signing off with excitement,
P.S.: I'm sorry I was mean about the Chicken Man. Sir Chicken Man? Sir Thou.