In America, if you don't contest any unauthorized uses of your copyrights, (and this is just my understanding) you lose the right to equitable returns; in other words, your right to be paid for said materials. In essence, if you have a copyright, you either defend it or lose it.
OK, this is going to be a rather speculative argument, but I do not think that this is at all the case. As far as I'm aware, this type of thing only matters for trademarks; even patents are allowed to go uncontested without losing them. Big companies would have you believe otherwise so that they have an excuse to sue, but I think a more accurate statement (corrected for British English, ho ho ho) is "In the USA, if you don't contest any unauthorised uses of your copyrights, you lose the much of the possibility of equitable returns; in other words, you are unlikely to get paid for said materials."
It is my impression that most copyright lawsuits are filed because they can
. The difference seems to be that in Japan, they have become accustomed to the fact that doujin works and the like are essentially a free avenue of marketting -- as the doujin stuff becomes more popular, they will see the sales on official
stuff rise alongside (hard to prove this stuff, though!). There doesn't seem to be any financial benefit at all in, say, Games Workshop shutting down fan sites
-- they do it because they want to retain control. They think they should be the only people with the right to run a site about their games (and make any associated money) and want to leave that possibility open for the future.
They can't both be right; it's either beneficial to sue or beneficial to ignore. Popularity of viral videos, the emergence of anime into the US market (quite probably due to fan subs), and so-on seems to indicate that the free publicity argument holds at least some water.
I should note that lawsuits have been filed over doujin stuff in Japan -- Nintendo filed suit over Pokemon H-doujinshi some time ago, for instance.
The result is that in America you can't 'squat' a copyright unless you're willing to defend it against any and all comers- but in return, you can't let anyone use your copyright without ridiculous licensing agreements. In terms of them 'not being the same game,' they use the same copyrighted characters, settings, etc. etc. etc. Copyrights aren't just on games.
Even the above being the case, there is nothing to stop them licensing the material at a sensible price, or for free. They may hesitate because it gives future comers a good bargaining point, but if you assume the possibility of future comers is low (as with an obscure game like the aforementioned one), that point is moot.
Apparently US case law says that characters are awarded copyright protection
. This seems wrong to me, but I guess that's just the way copyright law is. I'm not sure you can get copyright on a general setting or plot element, though -- that seems to be a bit too broad. Music remixes have a well-established system of forced-licensing for a small cost (which may or may not apply to use in games but I don't see why a game is different to a CD), but if the music is not a re-performance, you have to arrange a license manually.
Anyway, the depressing thing is that BlondRobin is probably correct -- while such games will stand in Japan, they will almost certainly get litigated in the US. Not only that, but there will likely be a cascade litigation into Japan which will hurt the Japanese
developer. It's not a can of worms anyone really wants to open, and one that should probably stay shut at least until the internet revolutionaries have burned the old systems to the ground. Or something.