You are really confusing me right now.
1. He isn't doing this for free. He has patreon. I highly doubt this dude is hurting for money considering he was making 3.5k a month in oct 2018 and has more than doubled the amount of patreon supporters since then. He is for sure not doing this for free.
And you really seemed to have failed to grasp my point.
Sure he could have had a Patreon if he had been just writing the plot. Do you really think he would be raking in the amount of money that he is now getting if he had just been working on the plot? You failed to answer that question. So let me try it again: if he was just developing the plot do you think, he would be making as much money on Patreon? Enough to pay all the bills so he could develop the plot for Waifu Academy full time? And if not, what do you think that would mean for the actual development of the game, let alone if there is / was going to be a game to be developed in the first place as a result of that?
2. Like I said earlier, I may be mistaken, but it doesn't seem like he has plot notes. At least ones that aren't very basic. He writes as he goes so I don't see how that is effecient.
First of all, you are mistaken: you did not say that earlier. Second of all, it is extremely likely that he uses plot notes. Extremely likely to have been (partially) written down, because otherwise he just has to mentally keep track of nearly a thousand relationships between characters in his head. And since power dynamics are at play, they are not necessarily symmetrical in nature. Never mind whatever else is going on in the characters' lives. That can be rather taxing, to say the least.
As for how advanced they are I do not know. But given the sheer amount of characters, with their own active lives, that is quite the task. This is not exactly a story, where NPCs do the square root of nothing until the MC shows some attention to them, after which the female NPCs will undress in a matter of five minutes for some sexy times. Which is extremely common in other games (maybe made slightly more difficult by requiring a fetch quest or two).
Without using plot notes, quality control processes would either come to a near standstill, due to everything that has to be checked for and accounted for, or it would simply show up in massive plot holes, or incoherent story lines. Neither of which has happened.
3. Not every character is featured in every update and people don't really complain about that. They just say they hope [insert character] gets featured soon.
Yeah, because pretty much every character gets featured in an update. And if a character misses out, plenty of other characters get attention. If it just say three characters, out of 2 dozen, that get featured in a short update (which is certainly possible with a 1-day update, depending on who gets featured), there will be boatloads of complaints. Even more so if some of the character development does not include sexy times. That might mean if someone is an Inori-fan, they would have to wait 6 updates or so before something happens with her. Multiply by a factor of two if said update does not include the desired sexy times. Don't think people will be that patient. You can see pretty much every thread of popular games with short update cycles for evidence of that. Or even worse, games that update slowly, and never advance the main plot, or include sexy times. Or even both. Yet some still retain massive following and support.
As I said before, Irphaeus could have gone about things more efficiently, if he had known beforehand what would have happened. Probably hire some help from the get go, streamline and automate processes more, get a specialised rendering rig and rendering scripts, and whatnot. But that did not happen. When you start a project, you can't bank on it being a success, especially not if you have limited means available to you (unlike say EA Sports). Can't really blame Irphaeus for not being loaded, can we?
The thing is, if he rushes now, everybody will be dissatisfied. But if he delivers a quality product, he can start a future project from a much better base, which would mean, among other things, a much shorter development cycle for a game. With the former, people will simply think that Irphaeus has laughed all the way to the bank, and not bother with Irphaeus as a developer in the future. There are long term benefits to both Irphaeus and players to the latter - and I do think that on the basis of the game thus far, Irphaeus has real potential, beyond WA.
6 months for two days is extremely slow, if it were a sandbox game. But with a visual novel, 2 days can be anything from 1% of the game to 50% of the game, depending on the scope and depth of the game. The revenge plot certainly does not necessarily have to take a year of in-game time. It will all depend on how Irphaeus plans to deal with that, and how long it will take to seriously develop the stories for the more neglected characters (for example, the abducted parents story line). And as more and more story arcs come to a completion, it may become easier to juggle the characters as well, thus resulting in an improved update time.
So your guess is as good as mine, with regards to how much time is left to complete the game. But as long as the quality is good, I can wait. It is not like there is nothing else to do this life.