@julesh This is a good question, and I'm not sure but something makes me doubt it (or, if there is such a framework, it is probably restrictive enough that all the logics it generates are overly similar).
I do think it is important to think about what the purpose of cut elimination is today — it is a technique that simplifies (1) establishing coherence theorems and (2) deciding word problems.
For both of these, I do think that the 'deep intuition' you mentioned is still needed, but 'the worst proofs ever conceived' might be avoidable if you are open to achieving these goals using tools other than cut elimination.
The thing about cut elimination is that you can have two presentations of the same theory, with one satisfying cut elimination and the other not. But every reasonable property of the theory (including presentability by cut-free normal forms!) is going to be invariant, so the calculus "from which you eliminate cut" becomes pretty unimportant, and what becomes important is specifically the cut-free presentation itself.
From this point of view, cut elimination recedes from view and we focus on the question of presenting by normal forms (which may be substantiated in ways that are more modular than cut elimination).