Minecraft is also slightly an outlier, I would say; its modding community has put a lot of work into making it easier for people to get started. It’s still a far cry from having a “view/edit source” button, though.
If I remember correctly the early days were painful as well, with it being necessary to manually unpack the jar file, and work with deobfuscated decompiled code. I'm not sure what the state of it is nowadays, but I hope its more pleasant.
My favourite game from a modding perspective is Kerbal Space Program. Just drop a Mono/.NET DLL into its GameData folder and you're good to go, and code completion works automatically during development as long as you have Squad's own DLLs in the right paths.
These days Mojang provides obfuscation maps, so you can work with proper class and method names (though no parameter or local variable names). There's also been a lot of effort been put into the tooling. Nowadays there exists Gradle plugins that will download the game jar, decompile it and deobfuscate it using the official mappings. You develop against the deobfuscated code, then the plugin will turn the unobfuscated names back into their obfuscated versions when you compile.
There's also been technology developed that lets you easily modify specific parts of a method in the game, so you can e.g. insert calls to your own functions at runtime.[1] This saves from you having to modify the game jar itself.
If you used the Forge development environment, then it did the deobfuscation for you. They have it set up so well you basically don't even realize it happened.
