The Transpennine 158 seats used the original BREL seat frames fitted with a new type of seat cushion, so it's the new cushions that made all the difference!
I also think it would be a good idea for some seats to be refurbished and to replace some of the poor ones in older trains such as the non-refurbished 142s and 150s.
This has happened in a limited manner, as when the Central Trains and Wales and West (later FGW) class 158s received new style seats, the original class 158 seats were refitted into those companies' class 153 units, which I think is a very good idea.
Also I'm led to believe that the first class seats in the SWT class 159/1s were reclaimed from the then "One" operated class 170s.
I imagine that these days, with "green" presurres a big issue that once the original seats are removed they are broken down into their individual component (metal seat frame, plastic outer frame, foam padding, etc) and recycled according to each material. I would also HOPE that a good few seats are retained by the TOCs to act as spares, although as the majority of Sprinter era units have now been through a refurbishment with new seats, there will be fewer and fewer units fitted with the original design of seats.
My personal favourite seats for levels of comfort are the Richmond seats in ex-Northern Spirit 156s and the seats on the Chiltern 168s.