i definitely agree that the broken scenes and whatnot should be cleaned up, that's not the kind of thing that should just be left around. you're 100% right that the implementation could use some work.
i don't agree, however, that npc quests should be made unmissable. to compare to other jrpgs, sidequests being missable as you advance the plot is extremely common, and i don't see an issue with it. to compare to other games on this site, it's not any different than missing a character because you chose to not go meet up with them when you had the chance; in fact, that's exactly what happens, just in rpg form rather than as a vn/sandbox choice. also, i always appreciate having the choice of which characters to pursue.