An automagic magic-button to arrange ALL of your flows into neat ordered stacks of flow-elements... would be indeed a kind of magic, since the flow-logic of everyone's flows are build-up based in a personal way for a variety of reasons.
But i do know exactly what you mean though.
I would suggest that a complete re-arranging of a flow should NOT be done unless your flow has fully gone through testing.
I'm not saying to not have your W.I.P (work in progress) flow a bit cleaned up while designing it... so that you can see what you're doing (quickly link wires to the correct element-nodes etc)
But really, making things all neat and dandy requires, in my opinion, a completely working flow.
Making a flow easy to look at while working on it... i would say to have it 'just' clearly enough to work with.
Although you CAN however extend parts of your flow to separate flows in order to reuse and refer to it.
This way flows don't have to be as big, and can take part of higher complexity because of stapling of flows (functions/subroutines)
But as far for the mess... this is true for all developing/designing in all sorts of fields.
Programming, VFX, whatever.
The creating process will always be a mess.
All creators share this nuisance i think, because we aren't 100% effective machines
