Welcome back! Thanks, yeah, I think those are all good points.
I think you're describing the MVC pattern, is that right? I think I'm starting to appreciate it more. You might already know, I currently separate out the data, because it made saving and loading the game easy and reliable. However, I still coded the view and controls sometimes pretty close to each other. It's definitely something I'll be more conscious of next time.
I think you have a really good point about how to replace permadeath, too. Before Darkmorrow Arena, I actually worked on another RPG, called Mournholm Castle. That game was modeled after Dark Souls, and you can re-spawn back at base, as many times as you want. The next game will probably be modeled after Path of Exile which also has the same thing. Using both of those games as design models, I think I'm going for the second approach you mentioned. The player can always continue after a failure, and accumulate power and equipment over time. They can take their time. But, they will need a strategy or find good equipment to challenge the later levels. That way, there won't be any pressure to perform, but there will also be something bigger to strive for. I think then players who want to see scenes are happy, players who want to collect neat items and try different builds are happy, and players who want to take on a challenge are also happy.