Melody Maker's problems towards the end were several. They mostly stemmed from its ridiculously over-zealous campaign to destroy all pop music and replace it with eighty shades of grey indie wank (ie: promoting worthy guitar bollocks like Toploader and Embrace over genuinely thrilling pop music).
The problem was compounded by an inflammatory cover based on a parody of a Craig David album sleeve which featured a lookalike sitting on a toilet with a constipated facial expression, next to the words "UK garage? My arse!". The cover was rightfully attacked for its borderline racism and probably helped alienate a sizable proportion of its readership.
Thirdly, MM editor Mark Sutherland's sinister re-invention as a kind of indie fascist proved to be the final straw for many, with his policing of the letters page every week by putting down all dissenters, praising those who slated chart pop and generally saying suspect things about "our music" and "the struggle" continuing as if his readership was some kind of Hitler Youth he was trying to motivate. Towards the end it only appealed to people whose idea of "alternative" music was a Jamie Oliver compilation, anyway. It was good for so long, but just before the end, it really deserved to die.