Arc doesn't have those kinds of resources, so two years making the under-the-hood work? Not really unreasonable.
Apples to oranges comparison would be me putting it lightly.
There is absolutely no way a ren'py based VN is anywhere as complex as a 3DS remake on a brand new engine of an ancient (in tech years) GBA game. There are so many differences in that example and this project listing them seems redundant, but I can if you insist.
The most glaring ones to make my point is that the staff that worked on Metroid 2 and the remake are not the same, neither was the engine, nor the hardware. CK is the same guy, same engine, same experience all the way through. Now, it is 100% correct that he is not as experienced as any of those professionals, but he doesn't need to be for the scope of this project.
The reason this project has stalled out is because of random, unneeded changes. It would be as if in Samus Returns they decided they needed to add a 3D racing minigame to progress from screen to screen, and then burnt years of dev time and resources chasing this bizarre vision.
Although I disagree with your example, I do understand your point. Solo deving is hard and its not unreasonable that the project has stalled. The unreasonable part is the way the time is being utilized.
This isn't the first time the dev has done this. If you search the thread, you'll find complaints and screenshots of when the dev downgraded/changed all the KK models for the girls for seemingly no reason. Thats a decent amount of effort spent recklessly. EDIT: The post above mine actually answers this and was posted as I was composing my own. That specific example can be safely disregarded, I somehow missed that while trawling the thread.
Whether it be perfectionism, a lack of proper idea of what to do next, overestimating ones own abilities, sheer laziness, burnout, or some combination of all, the end result is the game isn't being progressed in a tangible way. I personally remain hopeful something will change, but realistic in my expectations that nothing will. Perhaps one day a proper, high quality update will be released once more.