I've seen well backed arguments that the lowest lifecycle cost (maintenance) and lowest environmental impact surface (erosion, widening around low spots) for a well used trail/path/road is a raised, crowned & drained hard surface.
Has the NPS ever floated hard surfacing the C&O? Something like a polymer soil stabilized surface could be sensitive to the history/environment/aesthetic of the path.
I know, I know, all it takes is money.
Areas that have been resurfaced in the last few years are in pretty good shape and drain well. Many areas I ride close to home have been redone recently and are not a problem after it rains. I think a better technique has been developed within the past several years, using finely crushed stone and a thicker, more compacted layer, and most importantly, no dirt. But, there are still close in sections that become immediately muddy and do not appear to be a priority. Resurfacing outlying areas is a work in progress. The muddy areas are considered to be "self healing," which means after they dry and are used for a period of time, they become smooth again. So I would guess in the next decade the entire towpath will be resurfaced, which will be a huge improvement. In the meantime, it's part of the charm.