One issue is that while Innoxia is definitely not a professional making a professional product, I like to take a broader structural approach to these sorts of things and one takeaway I frequently hear from amateur programmers/designers/etc. is that Java is an absolute goddamn cesspit of a system and will murder every project of depth you will ever be able to dream of and initially implement. It just seems really bad.
There is absolutely nothing wrong with Java, just people who don't use it properly and then blame the language. The issue with this game is not the java language. It's how Innoxia went about architecting it. Why she felt the need to create an engine from scratch is beyond me, especially as a novice/beginner developer, and it shows. Using JavaFX for a video game is already rocky at best and she didn't even make use of the JavaFX UI Library.
Effectively Lilith's Throne is a web application embedded in a JavaFX application which is already going to cause considerable headache.
Her code was not made with extensibility in mind, as a lot of things are hard-coded and Enums are abused (until recently) pretty much every game object was an Enum. Her code is very disorganized, stuff is all over the place and the way it is organized means that with every new addition the time to develop increases exponentially. Not a very maintainable application.
Now all of this is forgivable, if you're a novice developer, you're a novice developer. You're supposed to make these sort of mistakes so that you can learn from them and grow, namely in a team-based environment with more senior developers to gather advice from.
Innoxia's failings is more due to the fact that she is a solo dev, and quite frankly the furry adult community is filled with these sort of devs because they realize they can make money while working on passion projects. Because of this she'll make all of these mistakes and not really know they're mistakes. There's nobody reviewing her code but herself, nobody holding her to good practices. And because of this those mistakes are allowed to fester until there's no going back. I think Innoxia realized that her bad development practices have caught up to her and nothing short of a full re-write is going to really solve these problems. And that saps your motivation hard.
Honestly if it were me, I'd of just used the libGDX library as the game engine, and then utilized the Artemis ODB ECS (Entity-Component Sytem) to build this game. Then made it purely data-driven with moddability in mind from day one.
EDIT: I should add that Java does have it's issues, but so does every other language made, there is no perfect language. It's just a tool and a tool is only as good as the person using it, and if they are using that tool for the proper job. The way Innoxia built this game, using any other language wasn't going to help matters.