I don't quite follow your reasoning here. If ToT, with all of its high quality CGs and complex RPGMaker minigames and systems, is being compared to a fairly simple, text-based, mostly CGless RenPy game... Shouldn't that speak volumes of that text-based game and/or be an overall bad sign for ToT?
Either way, I'm not saying MGD as a game is better than ToT (even though I believe that it is), I'm just saying its writing for the most part is.
While I understand your point about the setting ToT's setting being really shitty and limiting creatively, that's not enough for me to "cut Koda some slack" for the following reasons:
a) I don't see why he can't add backstories to the girls when certain conditions have been met. If he's not feeling like giving the player infodumps on their past all of a sudden, he could always construct small flashback-style RPGM segments of gameplay to tell their stories.
b) He should still be able to add interactions between the girls or other characters in the tower in order to flesh them out a bit (there's already a few "inter-floor" interactions, like in Yvonne's expansion, but they're pretty meaningless and don't characterize the girls in any way).
c) He can even give the girls random hobbies, quirks, eccentricities or fixations, really ANYTHING in order to make them somewhat unique and not as bland as they currently are.
And the most important one...
d) Koda doesn't really give a crap about the "nature" or the "rules" of the tower. Think about it, the setting has already been retconned multiple times. You thought floors were supposed to make sense structurally? Naga pearl magic says no. You thought every villainess was supposed to be of a certain element? Cobra randomly has two, Karen, Crow, Jess and Swan don't even have one. You thought there was supposed to be a single prisoner per floor, and that they were supposed to belong to different dojos? Floor 4 has a herbalist in it because apparently it's okay to eat your own prisoners and find a random kid in the woods to replace them with, Floor 5, 6 and 6.5 have sooo many prisoners it's not even funny anymore. For all we know they could reach Floor 10 and it turns out the tower was actually a dungeon and we've been underground this whole time...
Here you're just being unfair to the characters in MGD imo. Some of them totally are character archetypes of the kind that you'd see in anime, but they're either...
a) Simply done well. They're well characterized via their relationships and interactions with other characters, the trope that they're following is cohesive with the rest of their character, they have some sort of backstory, they can convey a great deal of personality, etc. There's nothing wrong with following character tropes as long as the execution is good. A good example would be Ancilla (aka Best Girl), your typical kuudere but written very solidly.
b) There's a twist. The character archetypes have an added complexity to them that makes them unique. Like for example Elena being the typical office lady that is bored to death of her desk job, except she copes by drinking which has turned her into a crippling alcoholic, or Lilian being this innocent genki church girl... Oh, wait, she's so much of a zealot that she openly engages in monster girl discrimination, seeing their lewdness as impure and vulgar thanks to her religion.
c) They're underdeveloped because they Thresh hasn't gotten to them yet. Trisha is supposed to become a full-fledged succubus at some point, until then she's a solid but kinda basic chracter. Mika used to be just like this but after getting her "character update" she became a lot more interesting, complex and harder to pin down as a single character archetype.
d) They're just bad. I can only think of Nicci and Kyra (both MGs that were released very early on) as completely, unapologetically bland and uninteresting characters, but even Kyra feels on par with Lily while Nicci feels on par with every other ToT villainess in terms of how one-dimensional they are.
e) They're a generic, unnamed NPC. Think the elves, the imps, etc. Feels justifiable to me that these are also kinda basic, but some of them are still top tier like the kunoichi trainees in all of their smug glory.
f) They're played for laughs. MGD can actually be pretty funny at times, which is another testament to the strength of its writing. Example: Perpetua, the GOAT.
And then there's so many other characters that go beyond any "anime cliches" by being so multi-layered and interesting, like Kotone, Mika, Jora, Amber, Sofia, possibly Venefica.
As a closing statement, to add to what bahamut said about Koda's fondness for doing the "I wasn't even using 10% of my full power during that fight" meme with many of his characters, Sofia does exactly that in MGD. But it isn't treated as an amazing feat of pure skill or sexual prowess in her part, instead it's contextualized as TRAGIC because of how combat works in that game. It means that she's so immune to pleasure that she can't be made to climax, which in turn leads you to the somewhat hilarious and emasculating realization that every time you beat her in combat and made her cum, she was actually just faking her orgasms. If that's not genius writing, and the perfect encapsulation of the gap in writing skills that separates Koda and Threshold, then I don't know what is.
Thanks for coming to my TED talk.