I'm really not all that bothered by the inherent production flaws; I view trying to actually alter the materials as rather unnecessarily invasive. it's this sort of mentality that Kawamori probably shouldered in making his alterations, and it's really plastic surgery gone too far. Serial Experiments Lain is possibly the only instance I can think of where something so drastic is quite welcome and commendable; I still pause at the thought of losing the original, but it is so sophisticated and clearly guided by the central creative forces of the original that it's not that troublesome. DYRL isn't like Lain. Considerably more time has passed and would pass before a hypothetical reproduction, and the original creative forces were fairly diverse; not only are we minus the late Ishiguro, but who's to say that Itano and Kawamori would or could work together? It's also no secret that the floodgates on Kawamori's shall we say, ideology, have really opened since; I'm sure Itano has changed too. Further, the original DYRL material is not SO bad. Despite a considerable amount of out of focus material, there is good stuff in there too.
Even if only the problematic scenes are tackled by artists trying to make a carbon copy with archaic production methods, they still might not be able to make something that looks authentic to the source. Moreover, if they were to muster the forces necessary to do so much work, they might as well remake the thing or just create something new altogether. "Fixing" something is necessarily a delicate procedure, and I'm not sure the potential benefits would justify the costs,especially if something new could be had instead.