I don't think it's just a "small niggle". Stuff like this, added up with various other things to do with passenger environment (like, say, stations with nowhere warm to wait), has an impact on how people perceive rail travel and make journey choices, and result in other modes of transport being chosen.
It's not something that in most cases would be horrendously expensive to improve - it just needs some people at TOCs (or whoever is specifying train interiors) taking it seriously.
As is mentioned up the thread, long distance coach operators, airlines, *some* railway operators in the UK and elsewhere in Europe, manage to get it right. The point about coach/air companies is important because they are the competition. Rail ought to be one of the most comfortable modes of transport - it has loads of advantages built in that can make it more comfortable - why throw this advantage away by failing to pay attention to lighting?
Services overseen by TfL generally seem to be OK - and probably reflects the relative amount of resource they put into passenger environment. They generally know what they are doing, but many TOCs just don't seem to know what they are doing.
It was rather disappointing to travel on the Greater Anglia 745s and find they have messed up on the lighting. There are lots of other things to like about these trains, but the ambience simply is not one of an intercity train. Somehow, they managed to approve whatever mock-ups were made of the interiors, without anyone questioning the lighting. They don't have the (weak) excuse that Scotrail has for its HSTs, which it inherited as is and can claim that modifying the lighting is too expensive or difficult. These are brand new trains. On their own website they describe the 745s as "very spacious and a high quality, sumptuous feel to the carriage". Not after dark - it doesn't feel sumptuous and high quality, it feels like a harsh and overbright environment, one that might be ok for an urban metro service for short journeys but not for jpurneys approaching 2 hours in length. Am considering making sunglasses part of my standard travel kit.