Yeah, I think I was totally misunderstanding the Japanese doujin game industry when I first started this. For example, EasyGameStation may very well have hauled off and made that Dewprism/Threads of Fate fangame and even sold it without permission or a license. That would easily land someone in court here, so it may have a lot to do with cultural considerations; and I'd be willing to bet that Japanese IP holders are pushing for tougher copyright enforcement over there nowadays.
I've done some digging into US copyright law, and from what I can see there's definitely no loopholes that would ease the way for a fangame studio startup. With music things are a bit different due to the existence of the "compulsory license" -- if you can't find whoever holds the rights to an audio track you want to rearrange, you just file a request with the US government and pay a fee & royalties as stipulated in law. Sounds like something a startup fan music studio could exploit to cut their teeth on, by reimagining some impossibly obscure work.
There's no such thing as compulsory license for most other types of media (I'm not even seeing one for books, which would presumably enter the Public Domain anyway, and I assume the rights to just about every gameworthy classic novel/short story have been bought up by some corporation by now).
So it seems a hypothetical "fangame studio" would absolutely have to negotiate directly with the copyright holder in every conceivable instance. The chances of hearing "yes" are obviously slim, especially since the whole concept as I'm imagining it is untried and the profit potential for the copyright holder totally unproven.
So the problem as I understand it is, the theoretical, world's first-ever American or European fangame studio needs something to cut its teeth on and prove the concept's worth, but has no opportunity to do so unless a copyright holder is incredibly, incredibly generous and open-minded. The typical corporation?...Not so much.
What I *could* see happening is a US or European financier negotiating a license with some artist of an original intellectual property (be it videogame, anime, manga, book, film, etc) who has inspiring and gameworthy material but is down-and-out on his or her luck as far as breaking into the professional market, or maybe has broken into the professional market but the property got drowned out amongst other properties, and therefore might be less costly to license. Preferably the source material artist would be from a third-world country where the US Dollar or the Euro would have a comparative purchasing power advantage, thus placing the property within the amateur Western financier's budget (say, <$100,000 to purchase the license). I haven't been able to find what kind of licensing costs
The Silver Lining folks had to pay, so I'm not sure whether this is unrealistically undershooting the possibilities or unrealistically overshooting.
That's quirky and unorthodox and ignores international licensing dilemmas that could crop up. However, getting past all that, if the source material were electrifying enough to gather professional-level amateur talent and the resulting videogame sold enough low price downloads -- hard copies are out of the question due to printing costs, and piracy would play heavily into the equation for better or worse -- to please the source artist in terms of royalties as well as keep the creative talent on board for a new project, then the hypothetical startup will have experienced its first "success." It will also have been a fan project in the sense that it's taken an original property and molded it into something new, even if the property being treated wasn't something as well known as a Chrono or a Final Fantasy.
The next step would be securing a license for a more mainstream but perhaps forgotten and not-often licensed property. Say, some cyberpunk anime that appeared on TV years ago but had limited exposure and is just sitting there in an entertainment company's portfolio, doing absolutely nothing. Previous success would be an ace up the sleeve of the fangame studio and thus serve as a bargaining chip, and away you go, until you've got enough property treatments under your belt to make a go at Square Enix's licensing and rights management department.
I wouldn't dare entertain notions of "living the dream" off such activities and making gazillions of dollars. However, I could see the hypothetical fangame studio doing a few economically useful things:
1. Generating a few extra bucks for people with professional-level coding, modeling/pixel art, and other talents who are already flipping hamburgers or otherwise seriously underemployed. They're out there, I'm sure of it. Every industry has people like this, and it's simply criminal.
2. Uniting said talent with demand that is being unsatisfied by the current videogame market.
3. Promoting market efficiency by delivering high-quality content at rock-bottom prices or comparatively rock-bottom prices.
One can dream.