Sooooooo, strap in a bit and I'd say like half of this is pure conjecture but, its what I've got from monitoring soooo yeah.
So I have absolutely no idea why he releases things as days and weeks instead of one massive main game, I have to believe it is because of his shitty code knowledge in the beginning, and this was his compromise. Blue's a writer and can do renders, but a coder he most certainly isn't by any means. I think this was his simplification system for how to manage the game and building it, until he got actual code help but now its just part of the quirk of how the game is built. Do realize I cannot confirm this information but I'm basing it entirely off what I know of Blue, and how is team is built.
As for what's the major issues with updates? Translations are a big one, writing it in German (his native language) and then having to have his proofreader translate everything and keeping his superb writing intact. This is the biggest drain on time, as Blue is not a native English speaker it would come out choppier and lose many idioms, metaphors, alliterations-you know all that cool wordplay and shit that makes stuff interesting. So all of Ecchi Sensei script needs to be cleaned up and read proper, this is quite a process as you might guess, you can render all you want, hell even streamline your code, but translations of this quality take time and energy to accomplish.
I know that's not specifically what you asked, but people in the past said Renders and code aren't that hard, and I have to make clear that this shit needs translated each time, and needs to be held to a high standards of narrative quality.
As for why this merge has taken forever? That's because we told them to work out literally everything they could find during a merge all at once, its a daunting task, and they had to tackle some very tough issues. Bluecat does not want this to be a simple VN, he wants it to be the greatest fucking experience of all time, he's got big ambitions for this and has a big appetite to make it into what he knows it can be. Sorry about how long its taking, but this is only the second merge, and its a massive beast to tango with.
The next merge will be six in game months, so we've still got at least a year and a half until we have to go through anything again-even then it might be super simple at that point. Also as a point, not every VN on this site just goes update to update, Mr. Dots is a known example of having split story parts up in DMD, as have other creators. It's simply uncommon to handle it this way, but merging does more than just smash everything together.
The merge will end sometime soon, I do hope, but until then just know that the reason why this is occurring is because the patrons told them to do it this way, and Bluecat is very ambitious and doesn't want this to ever be "just another VN". This whole thing is a big mess but once they clean it up, and ship it out. it'll be a nice polished stone for us all to gawk at. Until then please be patient.
I may have tangent off a bit, and I'm sorry, TL;DR-the game is made in a quirky fashion, that isn't unheard of with larger titles, and the reason the merges happen like this all at once is because Patrons said to do it that way to the Devs way back when.