There are some solid ideas here and definitely a commendable effort in creating a project in Unity with animated sprites, but I don't think the complete product really came through for me.
Breaking down by criterion, spoilers from this point forward.
Implementation of Theme:
I think what you're going for is the brightness of finding companionship in the melancholy of a post-apocalyptic world, especially from Donnie's perspective, who was literally just wandering before the events of the VN and now has made a connection that has at least temporarily made things better. Like, I get that, theoretically, but I don't think this is coming through strongly. Maybe this is because the characters aren't really deeply fleshed out here (more on that in a bit) but this feels more just like a temporary distraction than a meaningful difference in the characters' lives. Remy has his little speech at the end to try to sell the point more but, I don't know, it just didn't hit for me.
Story:
Two areas where I think this story could really benefit from improvement:
1) Natural character dialogue: There's a lot, especially in the first scene, of what feels like "checklist" dialogue. Basically you have a list of things that you feel like you need to exposit to set up the characters and/or the plot, and you're so focused on getting those things out there that the conversation feels stilted and unnatural, like the characters are talking past each other to get to the next point on the list. It's tricky to get right sometimes, but make sure every line of dialogue is smoothly flowing into the next line - when you do this instead of moving from exposition point to exposition point, you're more likely to get more of the characters' personalities across, which is something this story could really use. Right now there's not much to either character other than being generally friendly and easygoing. There's some backstory sprinkled in, like how Donnie was in the military, but we don't really get much of a sense for how this has shaped him or his attitudes about the Departation. You can also drop some details if they don't fit naturally too - going into the characters' full names doesn't add much other than giving them the chance to quip about it, and you can accomplish this with practically any subject. You don't need to reach to get there.
2) Exploring the setting: Easily the best part of the VN is the idea of a post-rapture apocalypse. That's such a fun thing to try and explore - besides just having the post-apocalyptic survivor narrative, you have the added complexity of being someone that didn't make the cut, for better or worse. Unfortunately I don't feel like we explore it much deeper than surface level - we get a sense that the characters are bummed about it (kinda) but also in good spirits (kinda) and that's about it. You mention them driving through an abandoned town - while they do that, use that as an impetus for further discussion. Go into where they were when the event happened, how it played out, if there's any idea of what caused it, how many people were taken, how they feel about it, how they coped, etc.
Other things to more quickly run through:
1) The sex scene was kind of awkward. Like, it's just a CG that pops up for a line and then fades out with no accompanying description. If you're going to go for the 18+ and have a sex scene, go all out. You can do it with the one picture (or two since there's a variation) but still have the text describe how the full scene plays out.
2) Ending felt pretty abrupt. I thought there was going to be more of a conversation where the characters further broke down their outlook on the situation, but it just kinda... ends. I didn't think the "post-credits" scene added much either. Like, yes, it's a reference to a line of dialogue that happened a few minutes ago, but it's not like a real zinger that has any punch to it. Just feels like a reference for the sake of having a reference.
Presentation:
One of the stronger elements of the VN to be sure. Clearly a lot of effort went in to creating the 3D models and their animations, and they look very good! Two things to note here are 1) while the animations are very nice, the sprites don't need to be moving all the time. During the laundromat scene there were a few moments when I wished they would just sit still; 2) you're already aware of the sprite disappearing issue. For how good the sprites are, I would have liked to see them during the car ride.
Main menu track was quite good, so it was a bit disappointing to find that there was no other music in the game. Really could have used it at times, especially in the car where it could have been passed off as diegetic.
A bit more random, but I'm not sure why the 18+ disclaimer appeared a few lines into the VN? Either have that on startup or as soon as you begin new game.
Creativity:
As mentioned above, the premise of post-rapture mundanity was the best idea of this VN, and I think it's a really good one. "Love at the end of the world" isn't necessarily super unique (I've seen it a few times now in this jam) but this could have been a really interesting take on the concept. This really just needed more time simmering with the setting and characters to really shine.
While this one had some issues that prevented it from reaching its potential, I can still definitely applaud the effort!