I think it would be nice for the livery to reference that of the LNER during the Grouping era as they're already doing so with their decision to use the brand. Many passengers won't know what the name references and will just think that it's a memorable acronym; similarly, using a small amount of Apple Green or teak-effect surely won't offend the aesthetic preferences of those who are unaware of the history of the ECML, yet would act as a knowing indication to those who get the reference. I agree that modern tastes demand something other than a copy of the old livery, and I think it would be unsuited to contemporary stock, but, for me, the Virgin red suggests a mere rebranding rather than a new era for the ECML, and, for those who take an interest in historical matters, red is much more a West Coast/Midlands livery.
I agree that travelling on a standard service in, say, 1932 somewhere on the LNER network was a remarkably unglamorous experience, but I'm not convinced that the LMS or Southern were noticeably superior. I exclude the GWR as, other than South Wales, most of their network was in areas with less of the smog and dirt of heavy industry than either the LMS or LNER and fewer dreary commuter suburbs than the Southern. I think the main problem was that the financial difficulties experienced by the LNER meant that, as you suggest, out-of-date stock and delapidated locos were frequently used on secondary routes and lightly-used branches after they ought to gave been withdrawn. Perhaps, though, the modern ECML services are much more redolent of the East Coast expresses than a Gateshead commuter service of non-corridor stock or a pair of Quad-Arts heading out of the capital behind an N2 on a wet winter's evening, so therefore the association is more apt than it might first appear?