I answered almost all of them. I won't be offended if you don't respond to all of them.
GENERAL:
1. Which one is your favorite?
I'm stuck between "The Art of Making Time" and "The Dove's Nest."
2. Which one is your least favorite?
Maybe Cat Thing, but not because I actually dislike it, it's just that I like the other ideas more.
3. Do any of these ideas remind you of something else you've played?
No. Granted, I haven't played a lot of VNs.
4. Is this way too effing long?
I suppose it does look a bit overwhelming, but you have a table of contents, and this is a
VN forum, anyway.
5. Should I break these into separate threads in the Ideas forum?
It's fine.

You could try putting the genres next to the names in the table of contents so people can just read about ones that they're more likely to be interested in.
THE DOVE'S NEST:
1. Which girl is your favorite?
Natasha, probably. I like motherly characters a lot I guess. haha
2. What do you expect to see in a murder mystery?
In a good one, I expect to see a complex case, with, as gekiganwing said, many possible suspects. Similar to cases from Phoenix Wright, the mystery should unravel at a reasonable pace and the perpetrator should be proven through the evidence they've left behind and through witnesses'/conspirators'/people that knew them's words.
3. Any other questions or comments?
You listed talents at the bottom, do you plan to implement (if you end up making the game) stat raising into the game as a way to progress through the story?
SEVEN WISHES:
1. What do you think about the concept of the genies moving through another plane to grant wishes?
I think that this is an interesting idea! I'm curious to see how this will develop.
2. Any ideas on why the planes have become unsafe?
Maybe something to do with paradoxes or evil genies?
3. What would you like to see in the supporting cast of characters? All genies, all humans, an even mix, an uneven mix?
I'm thinking there should be more humans, but maybe a few genies.
4. Should there be more romance options besides the main character's genie?
Maybe an evil Jinn/Genie? Other than that I think having one romance option is fine.
5. Main character name ideas?
Malia, Zera, Kayra? (IDK, my taste in names is different strange.)
6. Any other questions or comments?
What is the setting for this? The Middle East? If so, it would be interesting to read about different customs, cultures, and maybe even politics there. (I'm thinking that it could be like the Modern Middle East, but with variations that would fit with there being genies and whatnot. Also, perhaps not as violent. haha)
CAT THING:
2. What are your thoughts on my sound dilemma?
You should probably just use stock, cats don't all sound the same, but I think they sound pretty similar. I would just be careful not to overdo the sounds. Hearing "meow" every line could get annoying real fast.
AIRPLANE THING:
3. What's your stance on the idea of one vs. two perspectives and whether/how the second perspective should be incorporated?
I think this is a good idea. Switching perspectives can work well in a VN, I recently started reading a demo in the beta testing section that switched perspectives at the end of each chapter, basically you replayed at least part of the chapter as the other character. This wouldn't be the exact same for this game, but the second POV could just be set during the same time. (First chapter/act could only be one POV since it's likely the search team doesn't know yet.)
4. Any other questions or comments?
You have two #4's for this set of questions.
THE ART OF MAKING TIME:
2. Genders aside, what sort of characters would you like to see here?
I like it when their are a lot of races in a fantasy world, so maybe things like elves, orcs, or maybe you could create your own fictional race(s)?