What do you mean by "theme" in this context? I'm having a bit of trouble parsing it from a more literary context to that of a FG.
I assume you mean something similar to a more overarching-type "setting", but I really can't be sure.
I don't like telling players what they're supposed to do (this post totally doesn't count!) because that just feels counteractive to forum games, but I personally feel like people are in a way just missing the point and meat of the game.
I think he means that and also this thing you're talking about in the second quote. "You wake up in Hyrule, you are Ganondorf but also a magical girl" is the same setting but a different theme than "You wake up in Hyrule, Link is missing and Ganondorf has returned as a magical girl." It's what the game is about, essentially, and by extension why you should care about, be interested in, and partake of it.
Speaking of which, if you feel like players "aren't getting" the game, you might want to reconsider what you've told them about it. Too explicit is usually better than too vague, especially if your issue is that nobody seems to remember Ganondorf is supposed to act like a villain or that Hyrule needs protecting. That, to me, seems like a style mismatch: You thought you said "You're a manly villain magical girl, go destroy Hyrule," but players heard "You're a manly villain magical girl, do whatever lol." Which explains both why not many people are interested, and why the ones that are seem a little distracted.
Talking about Prints and Lone Galaxy specifically:
Prints starts out, in my opinion, unnecessarily vague. You don't even have the
year down, but it was obviously kind of important because you shot down Roman Adventures. This kind of "Do anything! Wait, not that! The other thing!" is not great for player participation and involvement, because it starts to feel like that point n click guessing game you're worried about. If you need something to be a specific way, say so; if you need it to be within a certain range or one of a set of options, likewise. "Select Period: Prohibition, 80s Cocaine Wars, 90s Rambo Style" is waaaaay better than "Select year: Not that year! I need the other year! You'll find out why it matters later."
That said, it was still a concise and interesting enough premise to garner a good number of suggestions, most of them pretty nice, in my opinion. Then you started them out in an apartment with a variety of overly specific knickknacks, and... well...
...one-time bump.
So to me, the issue here is that you killed your momentum. Everyone was all set for Roman Adventures and/or Something Else, they got Something Else, and then you took an entire update to mention they have $15 and ask what their profession is. You don't even specify if it's their crime job or day job! It doesn't feel like it's living up to its premise at that point.
And then everybody wants to go to the pub. Even after you explain that they've misunderstood. Which to me doesn't sound like they misunderstood, it feels like they have no idea where they are or what they're doing, and so are trying to get the game moving.
Well, you're at the pub. What now?
If so, I don't think it worked.
So after that point, you kind of get them re-railed, but by then there's only one real thing they can do, and that's blindly follow the lead you've given them. The sandbox is gone, as appears to be player interest.
If you want to get the game revived in its original incarnation, I suggest you follow some of the advice already given and flesh out the world enough that players have a box to play in. If you're going to track money, give it meaning. How much does a hunting rifle cost? Enough C4 to blow open a wall? A plane ticket to Guatamala where their next target is hiding? Without context, it's just a fiddly bit. Similarly, where does it come from? Jobs? What jobs, do you just look around? Do you have a contact? Are there multiple places you can work? Do jobs have success rates based on your skills and the conditions surrounding it? Where are those located? Then we get into how you find your targets to take revenge on them, and so on and so forth.
When in doubt, imagine the game as a control panel or UI. If they can't see a list of available jobs, they're probably not going to take one. If they don't know the Locate Jobs button exists to display the available jobs list for them, they're probably not going to find that one either. At this exact moment they have a giant targeting reticule over one of their Big Important Names, but no idea what buttons they're able to push, either to take the shot now, stock up advantages for later, abandon mission to build up and come back under more advantageous circumstances, or something else entirely.
For that matter, they probably don't know what their odds on any of those are. If they just jump out of the bushes and open fire, what's likely to happen? They hit nothing and then get their face shot off? They take out all four men? They engage a cinematic shootout sequence involving rock-paper-scissors style mind games over their next move? Looking at it myself, I don't really know, so I'm guessing others are similarly unclear. That adds to the uncertainty and thus disinterest or at least quiet.
I was gonna do something similar for Lone Galaxy, but that burned me out and I suspect you've gotten the gist of my likely complaints.