As mentioned by @jofemodo, very little of what we do is naive. We spend considerable amount of time considering and developing things. Please ensure you read this thread to understand the extensive discussion here in the forum during sooperlooper integration and testing. You will see that initially it was only really @Baggypants who gave real-life usage feedback. As a musician, zynthian user and developer, I can only develop what I think users want based on user feedback (and also, what I want - which can often be the impetus to start a development). Sooperlooper integration with zynthian certainly has room for improvement but redeisgning the whole of zynthian to make one user’s workflow work is not usually within our roadmap!
Regarding how chains handle MIDI input, like you, I too was initially confused. If I start jack then start a plugin then route MIDI and audio manually in jack I can do all sorts of wonderful things but… I will need more plugins to do some things and some of those plugins don’t exist… so I will have to write them… oh wait! zynthian exists and it does all this magic. Not the way I thought of doing it but it does it. So, do I carry on climbing the massive mountain to build the system I want the way I want it, or do I adapt and adopt the zynthian way? I chose the latter then, with words and actions I helped to shape it. Today’s zynthian is very different to the one that lured me in. Many people have been instrumental in shaping it and the journey is not over. We see out utopia, just beyond those infinite false summits…
Please do keep providing ideas and get engaged with development if you can but avoid heading down rabbit holes of major redesign without consulting our oracle (@jofemodo). He may pour concrete down the hole… he has done it before. 