I'm gonna attempt to answer all in one comment this time, so get ready for a gigantic wall of text xD You'll have to let me know if I miss anything, but I'll do my best :3

SPOILERS 

I never actually gave the MC a canon name (probably cos I'm the kind of player who likes to self-insert, or make a character up to roleplay as) so yeah, she doesn't really have one x3 I probably should have given her one though really! There's a tiny variation in the creepy guy's lines at the end if you name the MC Anathema though :D

Yeah, S**** was pretty much referring to all of the Kuro's as a whole cos he just hates them, even though it's not even their fault that they are the way they are :( With the first Kuro's, I didn't mention anything within the game, but I like to think they just started out fairly normally, without making too many personality changes, but then (as you said) the Kuro would become more and more messed up over time with all the cruel things happening.

 They definitely would have had some Kuro's though which they would have altered right from the moment of waking them up cos they were doing all kinds of tests down there, and would have wanted to cover as many things as possible. Also, with any of the Kuro's, if they're not seeing the sorta results and reactions that they're looking for, they would either tweak them to see if anything different happens when they change parts of his personality, or they will just terminate if they think a unit is a lost cause (apart from Dollmaker, who they just sorta abandoned instead >.<)

Yeah, you're right that when Kuro disappears at the end of the princess route it was because they pulled him from the simulation :3 The main thing that would have lead him to realise the scenario was close to ending was the defeat of Kai. Cos in each scenario there is a big challenge that the pair are tasked to overcome, and the scenario only ends in success if they manage to be victorious. Usually, they will keep running the scenario when things go wrong (like the bad ends), they will only retire a pair of clones if they are just hopeless. Even then, they will just attempt to run the same scenario with a different pair. So since Kuro has more general awareness of how they run stuff, he knew that the big bad of the scenario had been defeated and it would all be over soon for them in that world :(

With the bad end about knocking on the door, there was that and a few others where I was worried that maybe it would give too much away too soon by having Kuro hint at things with lines like that, haha. But the reason he tells MC she can do better next time is because he knows that the folks in the lab will just patch MC up and they'll go again. Pretty much all the bad ends in the initial 5 routes are simulation fails, and so Raine just oversees everything and attempts to guide/comfort the MC after she dies or makes a wrong move, then prepares her to be reinserted into the scenario to try again. Kuro knows that that's what's happening, and it's almost like his world is on pause while he's waiting for it all to continue. Kuro knows that MC will likely make it to the end of a scenario victoriously eventually, because Raine is essentially pushing her forward all the time towards the end (cos they do want the pairings to succeed, but each simulation is like a new test of their abilities.) The Kuro's generally know that when MC dies in the middle of a scenario/simulation, she's technically gonna survive, but watching her go through all the horrible stuff properly messes him up >.< Hence why he's sometimes the cause of the bad ends x3

Yeah, Tim's voice acting was awesome throughout, but in the scene you mentioned, that whole speech in that bad end was just delivered so brilliantly! That and some of his other lines actually make me cry a little when I listen to em cos he has so much emotion in his acting :3

You're right that Kuro just wants to save the MC by any means possible. He hates seeing her suffer, and hates himself even more for losing it sometimes :( He just knows from the few feelings he has leftover/passed on from S**** that him and MC are supposed to be together, he loves her with all of his heart, and he just wishes that they could be free to love each other in a place where neither of them have to hurt. Instead, he knows there's pretty much no way out for them, so all he can do is make the best of a bad situation and try to have some form of a relationship with her inside the simulations.

Also, if there weren't that many bad ends, I think that maybe it wouldn't come across as well as to how much they have suffered on their journey. To be honest, I would have liked to have made even more routes, which would have lead to even more bad endings, haha. Like I wanted there to be a whole route for the Idol and the Cadet scenarios, but I was too short on time with having Tim able to continue voicing Kuro since he was moving to Japan for a new job. It's probably a good thing that I didn't make the game any longer than it already is though, cos it took years to make >.< and I feel like I probably should have made something much smaller for a first project xD

I'm a huge lover of bad ends in any kind of game, but they seem to be in visual novels more than anything else :D I don't really mind what happens in them, but like you, I only like them if they make sense as part of the story, ones that are just jammed in without any real reason just get on my nerves >.< haha.

Yeah, that bad end in the detective route where the MC is trapped is one of the more emotional ones of the route I think :3 Like you say, the snow reminded her of Kuro, even though she was losing all of her memories, because of it being icy like him.

I'm super thankful that there are so many free resources available to use online for projects like this, cos it wouldn't have been the same without all the soundtrack and SFX, and almost all of the music and SFX I used was free stuff that people have just created and then given to the world to use :3

Funnily enough, I can't even remember why I decided to make Kuro icy cold to the touch in the first place! It just sorta ended up sticking after I wrote it for the first one, haha. I think it was possibly because when I first wrote the student route many years ago, I didn't know for sure what I was going to do with the overall story, and I think maybe I was actually originally going to have Kuro as a real spirit or something. Instead, I ended up making a lot of big changes in my head to what I wanted the whole story to be, so Kuro ended up being referred to as a spirit in a lot of the simulations, even though he wasn't really one in reality.

The detective route Kuro's way of giving power was my favourite :D It's my favourite route in general, aside from the hidden one! I'm glad that it made it feel like each route was a whole life of its own, cos that's how I wanted it to come across :3 

Writing character interactions is my absolute most favourite thing to write <3 I remember waaaaay back when I was in school, I loved English class, especially when we got to do fiction writing. The teacher would always have a go at me for my stories though, saying that I wrote too much dialogue and not enough of anything else xD That I should spend more time explaining what the characters are doing rather than what they're saying, haha. That used to annoy me, cos when I read books as a kid, the dialogue bits were always my favourite x3 When I first discovered VNs and saw that they contained more dialogue and character interaction than a typical physical book, I was in heaven immediately x3

 It makes me super happy that you love the way the characters were written and their interactions <3

That's good if you like reading my explanations :D I worry that I ramble on way too much when I'm trying to explain anything, and that most people will get bored and wish I would shut up x3 hehe.

I'm kinda glad that you think Kuro and Ukyo are similar, as Kuro was actually slightly inspired by Ukyo! :3 Amnesia was the first non-mobile VN I played many years ago, and I liked it a lot! Ukyo's story broke my heart, but I really loved it. With Kuro and SR, I sort of wanted to capture a more intense version of the sort of pain that Ukyo went through in Amnesia. I just loved Ukyo's story so much and wished there was more of it!

I'm happy to hear you like that feature after finishing the game where the music on the title screen permanently changes :3 That tune is pretty much the creepy guy's theme. It took me a few days of headaches to get it all working properly, haha. At one point, I thought I was gonna have to give up, cos there were a few bugs that I just couldn't figure out how to fix, but I got there in the end!

In regards to music, I really enjoy giving specific characters, or moments their own sorta theme, haha. That piece that you're talking about is called Unwritten Return, and the description of the piece on the site I got it from suits S**** very well :D This is the description:

"Dreamy and edgy; Not a combination you often find, and yet - here it is. The ambiguous and slippery nature of the piece are a wonderful thing. Perfect for scoring a character where the audience is unsure of them. Could be good? Could be evil? WE DON'T KNOW!"

If you want to listen to it any time, this is the website it came from here.

That's the place I used for most of the soundtrack! I spent weeks combing through the huge database of amazing tracks there, picking out all the ones I thought would fit well with SR :3

As for the title music being used in the hidden route too, I really wanted to do that because I absolutely love it when games have a main theme or title theme that is used during important moments of the story later on :D I haven't seen it in that many games, but every time I come across it I just love it so much! So I had to do it myself, haha. If you ever want to listen to that piece, it's this one.

To answer your last question, the creatures that pretty much destroyed the surface world were all actually spawned from the faulty experiment that Isaac released. I know I didn't really go into much detail about that in the game (again cos I was worried people might get bored if I included too much lore/backstory >.<) But yeah, the experiment that Isaac set loose to test went rogue, and they were unable to recapture it, so it just went completely outta control and spawned a tonne of thralls which it used to destroy most of the earth's surface. Really it was just doing what it was designed for as well, because it was an experimental bioweapon for human warfare. When humanity decided to retreat underground though, it decided that it couldn't be bothered to pursue them, instead choosing to live in relative peace after it successfully cleared out the surface of the world. Killing the creature would have killed off any remaining minor creatures that might still have been around, cos the creature which was the sorta last boss, was in control of all the other creatures, kinda like a hivemind type thing going on (like how when you fight the guardian outside the tower where the big creature is sleeping, that guardian has very little will of it's own, it's more just a puppet for the big creature.)

So yeah, like you say, by defeating the main creature, S**** and MC pretty much saved mankind... which technically means that Isaac actually succeeded in his quest to create a powerful enough weapon to save the world, even though it was his fault in the first place >.<" At least he fixed his mistake I guess! Though I'm pretty sure he could have found a much less cruel way of defeating the creature xD 

But yeah, humanity should be safe from that particular threat, and it falls to all the survivors underground to begin the process of starting again like you say :3 I wonder if S**** and MC would take charge of rehabilitation, or if they would decide that they've been through enough and just want a quiet life, leaving others to work on that while they have a well-deserved break, haha.

I hope I managed to answer alright anyhow :3 Feel free to let me know if I missed anything! Thanks for all of your questions + have an awesome daaaay :D