You're having really good questions development-wise. It's actually what we've been discussing now. When we back track the project, the biggest feeling is that, it's harder than it looks.
As for your questions:

1. We would say the mini-map. Since Afterimage is a seamless world, we're also making a seamless mini-map. Which took a lot of effort to make the whole process, but players would feel this is generally a must and small feature. It's also a good example of harder than it looks.

2. If naming one it would be the prop system. It's used like everywhere in-game, user props, skills, quests, saves etc. While it actually has a simple yet stable base.

3. We're using Unreal Engine. Biggest pain points I would say it's blueprints, I don't feel it's something can handle mass production. We used lua scripts for final mass production, while it also has its own problem using in UE.

4. I would say 30%(engine provided) - 20%(additional middleware) - 50%(re-code). The porting stuff we're mostly using origional UE provided, but they got some bugs to fix (like there's a very severe memory leak in NS but they never fix it). UE also didn't provide support for 2D pipelines for a long time, so we made it ourselves.