I prefer world-building that is "like reality, except where noted". If you have something about the world which works differently, because the fundamental difference is important to what the players are dealing with (such as functional magic, or other planes of existence), then that's great. If you have something about the world which works differently, because you want the world to seem less like our own reality, then that's just gratuitous.
The further I need to suspend my disbelief in order to buy into the story, the less willing I am to do so. If you get so far out there that gravity and light begin to work differently, then you've lost me. It would be difficult for me to relate to anything that takes place in such a setting. There are plenty of other worlds for me to explore, which don't ask for such a significant buy-in.
I prefer to use fantastical physics because they make more sense when fantastical things exist as part of the world. For example, it makes zero sense for there to be elemental beings and planes based on the four classical elements if the world is composed of the periodic elements. That’s what I loved about the Nephilim game, since it ascribed elemental associations to absolutely everything, even inventing new elements like Sun, Moon and Orichalcum to explain gaps.
But I understand your complaint regarding getting lost. So I keep this stuff under the hood, so to speak. My fantasy world building outwardly resembles the world as experienced by you or me, even if the underlying physics are completely different. It only comes up when I want to do things that aren’t possible in “lazy” worlds, particularly regarding spirituality.
It would take a while to explain, but at the moment probably the most visible departures I took from reality are magical fields (a la Nephilim, Warhammer), a hierarchy of gods/spirits who manage every aspect of natural cycles (a la Exalted), and by extension treating illnesses as spirits (a la Glorantha). To put it together, the magical fields give rise to the world and its spirits/gods, and the interactions of those spirits/gods cause the natural cycles. Rain, for example, is caused by thunder dragons straight out of Chinese myth.
This creates new avenues for characters to interact with the world. If a villain wanted to, they could cause a drought by killing the local rain dragon or river god. Thus setting in motion a quest to find a new spirit/god to replace it. To me, that feels more like mythology and folklore than the overwhelming majority of published adventure paths.
Initially I was inspired by this old article:
http://www.darkshire.net/~jhkim/rpg/magic/antiscience.html
Well, here's the thing - those pre-modern societies didn't think that way... but they were also *very wrong* about what was actually happening in the world. And, since they were wrong, you quickly find that if you follow their lines of reasoning for any distance, they become self-inconsistent.
I'm a physicist by training. Putting together a world that runs on fundamentally different physics, but has the characteristics you see in the real world (like gravity, and light, and such) is very, very, very hard. I don't recommend it.
I agree with you. So I generally only address the stuff that would relevant to gameplay or world building (as I use a similar approach in my fantasy prose writing). There are a few aspects of this to unpack and address.
Firstly, even the standard generic fantasy setting is inherently implausible. No ecosystem could ever support a menagerie of such destructive monsters. So rather than positing some kind of nonsensical ecology, I use magical physics as a literal god of the gaps. As a matter of fact I’m developing an entire pantheon of literal gods of the gaps (which is really the only reason I personally see to have gods around at all). For example, there is a god of evolution and a god of spontaneous generation; the latter gets ideas from the former, explaining why animals which were spontaneously generated resemble animals which evolved in reality. Animals which don’t follow the evolution god’s suggestions account for the various chimerical creatures roaming around, like owlbears, griffins, platypuses and the sharktopus.
Secondly, positing fantastical underpinnings of a world makes you engage differently with that world. You build it that much more fantastically. The idea that the heart is the seat of emotion dates back to Ancient Egypt and is still a common metaphor today, and making it literal doesn’t make a difference except in the case of things like stealing or freezing the heart. A person whose heart was stolen would, for example, be unreceptive to emotional manipulation. One might imagine an army composed of fearless soldiers whose hearts were made of bronze to exploit this. Fantastical symbolism is awesome like that, and I’m constantly disappointed more fantasy authors don’t do that.
Thirdly, when I take obsolete scientific theories from our own history and apply them to a fantasy context, I do take care to sanitize them if necessary. Some instances are... really politically incorrect?
To use a vulgar example, the ancient world had some very sexist ideas regarding the purpose and generation of semen. The feeling of tiredness after sex and the ejaculation itself were conflated into the mistaken belief that every ejaculation was hemorrhaging a man’s lifeforce (which some people still believe to this day); this is where the demonization of masturbation originates from and the idea that succubi steal life force comes from (i.e. succubi don’t have a special ability to steal vitality, this is a flaw of man; explaining why incubi don’t do the same to women). BTW, women were considered to contribute nothing to their offspring, although obviously this wasn’t consistently adhered to as shown by the existence of political marriage. Of course in reality we now know that masturbation is healthy and flushes out deformed sperm. A magical explanation would, for example, be that the prostate semen has a distinct pool of life force, one that rots due to its sluggish connection to the heart’s circulation of life force (in Ancient Egyptian thought, the heart circulated ALL bodily fluids).
Tying back into my “illnesses as spirit possession” mentioned above, I likewise reject the ancient world’s widespread belief that illnesses were punishments for immorality. Even if illnesses are caused by spiritual possession disrupting the subject’s humors, those spirits are as amoral as any real pathogen. Tree spirits have inscrutable plant thoughts and even the most convincing argument for peace will not sway a war spirit. BTW, this means that there isn’t a distinction between mumdane and magical means of healing, as both would involve spirit combat. (Thank Glorantha for that.)
Fourthly, I dislike the real physics with magic tacked on argument because it is used to keep fighters from getting nice things like the tome of weaboo fighting magic. If a zero-level peasant can cast the evil eye without conscious action as in real world folklore (known in anthropology as a subset of “magical thinking”), then it becomes that much easier to believe fighters can become weaboo fighting magic-users just by training really hard. The underlying magical thinking also ties more generally into the underlying animistic cosmology I adopted.
As always, your mileage may vary.