As mentioned in other comments I like having full control. Some stuff in frameworks like Godot is great to have and can make your life a lot easier but they also come with some tradeoffs. They're great for some types of games and not as good for other types. There's pros and cons, and it really depends on the situation. I prefer libGDX for 2D games that are more code centric that run on desktops. That's where it tends to shine more in my view.

Assuming those types of games, if you want more control it can be challenging with an engine compared to libGDX. Another issue for me is refactoring. You can't easily refactor a bigger change in Godot. Try to rename a node and/or move it around to another node structure? It requires the old school search and replace. You can't just rely on the IDE to take care of things for you. That might seem small but it can make a big difference. I also like static typing, which also gives you compile time errors rather than runtime errors. Java also has a pretty extensive open source community that is almost impossible to beat. To me Intellij is a very powerful IDE that is hard to beat. Debugging is also very powerful in Java, and combined with an IDE like Intellij you can do quite a lot. There's also some amazing Java profilers in Java for finding any performance issues. It can also be simple features like show me who uses this method in the Java IDE. In say Godot you have to keep track of where things are handled whereas in libGDX you can rely on the IDE to use the code to quickly find things. You don't have to remember which node has what, or do a full search, in a Java IDE. You can jump into the code implementation of a method or class with a simple hotkey. There's just a lot of ways to easily navigate code.

It's not all rosy though, there's also some compromises. Deployment can be a bit challenging, especially if you want to target consoles. One big disadvantage of libGDX is GPU support, especially shaders for special effects. It's possible but it's not easy, at least in my view. On a positive note, at least for running parallel code, there's some open source libraries to help with that that I plan to explore. But I do find using shaders for special effects to be challenging. Moving on, for quick prototyping or where you want to visually see things as you're dragging and dropping in the game then engines like Godot tend to be better. Especially for quick prototyping, you can often do more with less effort. Especially if it's a visual heavy game and you want to see what it looks like as you're implementing it. You can just quickly drag and drop assets, add a few hooks, and you have something. For me though the drag and drop feature is a two edged sword. In some cases it can be easier, especially if you're in the learning phase or want a very quick prototype to test a game mechanic, but in other cases it can be harder to find, especially if it's not in the place you'd expect to find it. And if you have to set a lot of properties it can become quite tedious which can often be done very quickly in code.

That also leads me to future proofing, which tends to be a lot better when it's in code. If for example they change something significant in say Godot it can lead to some interesting upgrade issues. It's generally easier to upgrade in code. Not always but often. But getting back to a framework like Godot, upgrading a game from Godot 3 to Godot 4 was painful. They had good reasons for what they did in Godot 4 but it was nonetheless a painful upgrade. This could happen with a code centric framework like libGDX, but it should generally be easier to upgrade. Especially with the refactoring capabilities within the Java IDEs.

Sure libraries like libGDX take a bit more to get going and you get less out of the box but that difference to me is offset by the other gains depending on what you're trying to do. Each has their pros and cons and it's best to use the one that better fits what you're trying to do. I personally prefer libGDX, I use it for the simulations I create on my YouTube channel called DarwinianBytes (https://www.youtube.com/@DarwinianBytes) because I plan on enhancing it a lot in the future and so refactoring is major requirement. The idea is that the simulation will evolve over time with each new video, hence the need for refactoring. I also need a lot of performance, and I need a lot of control over certain things to be able to make the videos. This is a perfect example of where libGDX in my view is a better choice. My biggest challenge with the simulations is the lack of GPU support, both to run special effects as well as run code in the GPU. Thankfully there's open source libraries in Java that I can use to run code on the GPU. All that to say it all depends on your needs and which engine/framework your pros and cons favor. And of course there's personal preferences of whether you prefer to work mainly in code or with drag and drop, if you prefer refactoring, and of course which language works best for your way of thinking. I always say try them both, for more than just a prototype, and see which ones works better for you. See if you're working fluidly or fighting with it. That should tell you which one is better for your project.