AFAIK the biggest problem with the R class was that their machinery was wearing out.
For example in the Indian Ocean in 1942 Somerville had to divide the Eastern Fleet into a fast squadron built around Warspite and the aircraft carriers and a slow squadron built around the 4 surviving R class battleships.
So with hindsight perhaps the R class should have at least had new engines fitted. In addition to being more reliable more powerful boilers could have been fitted in the same space for a higher maximum speed.
Fresh water production was a huge problem for them, particularly in the hot Indian Ocean. However, the main problem with the R class BBs was that they were a wartime expedient design and were built specifically for short range operations in the North Sea and given the limitations inherent in their design their long term growth potential is limited. For a resource strapped country like Great Britain in the 1930s, significant upgrades to the Rs quickly reach the point of diminishing returns and the money is much better spent elsewhere. Their singular use in WWII was as convoy escorts and old HMS Ramillies even sent the Twins packing and for convoy escort duty they don't need expensive upgrades. They are good enough to scare off or outright sink anything the Germans might send at them not named Bismarck or Tirpitz.