We have been fixing the flaws for years. The thing is, apart from the Gml related problems, GG2 simply has a bad codebase. It was originally written by a total GM newbie in hacky, throwaway code since obviously nobody would care about it anymore two weeks after the demakes competition was over, and there was a deadline to meet. Only that people embarrassingly did continue to care, and so the code was extended, by developers of somewhat varying skill. As a result we have a huge mess. Some parts of it get cleaned up now and then, but whenever new stuff is added it has to exist in and interact with the remaining mess, so it becomes part of that mess and reinforces the existing bad structures.
Just as an example, take a look at how game modes are implemented. It's horrible imo, but it works, so and the next game mode will be created the same way, probably by the time-honored method of copy, paste, modify. This cements the existing mess, because now if you ever want to implement a new system for game modes, you have to consider and rework an additional one.
Imo, the only way to actually fix this is to start from scratch with a solid foundation. Whether it is worth fixing depends on whether the project will be worked on much in the future, but conversely the future of the project might also depend on whether this is fixed - having a solid codebase could make development much less painful and more fun.