Honestly I think the problem you are running into here is more of a general culture opposition and conservation of detail working together to make things not show up more than anything that is actually indicative of some sort of trend. I mean if I'm a religious person making a game I probably don't want to highlight the fact that there isn't a bit of a shred of evidence for my fictional religion; such a thing is far to close to what real opponents of religion do all the time. Additionally we're seeing a hard conservation of detail on top of this. For religion to be really worth mentioning, it probably has to play on the story at some point, else pretty much the only times it's going to be showing up are in offhand mentions. That means if we want any sort of "serious" appearance of religion it's going to certainly be a main focus of the story, and that limits our choices drastically, and honestly the only plots involving religion seriously that don't outright go one way or another that I can think of are:
1) A story about a person struggling to stay faithful in the lack of evidence
2) A political story investigating corruption in a religious organization
3) A story about someone's conversion to a religion
2 is probably not going to have said religion match the protagonist's religion, and stories 1 and 3, while matching common religious media plots, are honestly pretty weak stories on their own.
It's basic conservation of detail, if the player's religion or an organization's religion isn't important to the plot, then it's something that can (and should) probably be cut out to emphasize the important parts, and will almost certainly not be mentioned more than in passing (which is why we have tons more games where religion is simply not mentioned at all). If the religion is important, then it's usually either focusing on the human side of things, or it's focusing on the religion itself, which tends to lead to plots that are either trivial propaganda, extremely controversial, or actually come out and declare the god's existence or not. As such I really feel that the best you are going to get in that sense are going to be things like a fair number of the Fire Emblem games where people toss around the words "goddess" in casual conversation or curses to note that it really is a widespread religion without ever giving any evidence for or against them (yes, I know about Radiant Dawn as an exception to that, and I'd like to note that just because priests are the common staff wielders in those games doesn't mean that they are wielding "holy" magic, sages can wield staves too, and staffs aren't any different from tomes in their notably vague source), or you are going to have games that look like any of the many religious propaganda games, which pretty much have never met any sort of real commercial success.
TL;DR: I'd add one more category to this:
Religions in games seem to be divided into:
-There is a god. She's right over there. Be nice to her or she'll kick your ass.
-There is a god. We pray to him and we get points/spells/healing.
-Some crazy cult-ish or “primitive” (or at least non-human) group believes in a god, but the PC (and the player) knows better than to buy into that nonsense. It's always a “haha, look at the stupid fools believing in a god that isn't real!” sort of situation.
-Games in which religion is widespread and believed in seriously, but simply isn't relevant to the plot, and thus doesn't show up much
These are usually going to be games where all magic has a confirmed or heavily implied single source (such as in Fire Emblem, or many of the Tales games), since the default is often to have "holy" magic like healing come straight from the gods (thus implying their existence), but they do exist.