That's interesting. I didn't think copyrights had to be defended. I thought that was a just a myth. I think Nintendo's official policy is to ask that fans not make fan works (and may be the reason there are so many Pokemon and Mario clones out there), but if that's the case, why are there whole communities dedicated to these sorts of things? Like I said earlier, if there's such a huge risk, why take the risk to begin with?
Copyrights do have to be defended (in most jurisdictions) in order to hold any clout. But ignorance can be a reasonable defense when the derivative work is obscure. If a fan game is released and 50 people ever see it, and the copyright holder doesn't pursue it because they don't even know about it, that doesn't give someone else the right to make a huge commercial project that's a derivative of the original and point the finger at the copyright holder for "not defending their copyright before".
You also don't need to defend your copyright in any particularly vigorous matter in order to protect it. If something's not hurting you, a simple cease-and-desist letter is usually all you need to issue, I think. Even if they don't take it down and you don't go after them, you can demonstrate your intention to protect your IP.
That does explain a lot, though, as writers make their living off of these characters and worlds and my guess is fan fiction writers and fan game designers might be completely ignorant of how the writers view all of this. Either that, or they don't care. Maybe they expect their games to stay in the community, be played and judged by the designated testers, and never really move beyond that. They aren't trying to sell anything after all.
If a fan wants to be sure that a work they're going to create (based on some copyrighted work) is okay, the onus is on the fan to contact the copyright holder and inform them of the intention to create a derivative work. Most of the time the copyright holder will say no, so that's why fans rarely reach out. But yeah, if the fan doesn't do this, and then the copyright holder tells them to cease and desist later, that's the fan's fault for not checking in advance. They don't have a leg to stand on if they say they couldn't have known whether it was going to be okay - of course they could have known, they just didn't want to know.
It's also surprising, assuming the Pokemon clone I downloaded from the app store is legal (I would hope so considering it's a popular game), how close you can come to the original source game and still call yourself original. The one I decided to try out had very similar game play, turn based battle systems, semi-random encounters, monster design based on actual animals, like in Pokemon, similar looking healing centers for the monsters, evolution systems based on levels, etc. It felt very much like a first or second generation Pokemon game with updated graphics and better game play, really.
Indeed, it can be surprising how much you can get away with. Look to other genres like Match-3, RPGs (think about how many early console JRPGs were mechanically similar to Dragon Quest), and Rhythm Games (think DDR vs. In The Groove vs. Stepmania). An exact clone of your gameplay could certainly be shut down (a Russian clone of Super Mario Bros. using different graphics but identical level design, for instance, was eventually taken down from the App Store), but it's really the "artistic" elements (graphics, music, characters/dialogue) and the core technology (if it's proprietary rather than middleware) that have the strongest protection in video games. Developers get a lot of latitude to slightly alter, or even directly copy, gameplay mechanics.