Proper API documentation
Why there are so few good mods is easy. There are few really good tutorials for modding. Best ones out there are character mod tutorials and well there is plenty of those. Anything harder there is simply no guides available. Coding is hard for most beginners who get easily discouraged when they are not able to understand how to search answers and examples from games lua files and if they don't get info from forum posts. API examples file is all nice but I think it would benefit everybody if we had api docs similiar to laravel api docs for example. Containing best practices and also list of prefabs, components, widgets, anims etc. Also would have examples how to add most types of objects and items into game as a mod. Yes its nice if people learn from other people, but what I can see is that often looking other mods can lead to fact that another mod is launched with same cardinal mistake as the one that was taken as example. This is where best use cases and best practices come in play.
Well also problem is that there are almost no good IDEs for lua. There are some that are good multilangual ones, but it would be nice if there would be some plugin or IDE that would be able to grab classes, functions and files from data folder and give code completion and function generation functionalities as well as different file template generation capabilities like most of Intellj products do.
Better Mod loading
Current mod loading is so random and unhelpful. Currently people have no control over mod load order and also game does't check issues that could arise form mods being incompatible. Due to the fact that some modders disregard guidelines that are basic for any programmer just because they haven't programmed anything before is also the problem of not having proper guide on how to do stuff and what not to do that would be definately in the API docs I mentioned before. Game should also protect player from such issues as a game breaking bug can show it's face at day 200 when somebody crafts a item that causes a conflict with other item in some other mod.