Wagons seem to be relatively late to widespread adoption despite their invention centuries earlier, despite having twice the cargo capacity they were not widely adopted until later. What was responsible for the carts longevity as the primary cargo transport vehicle?
Generally, a wagon doesn't have twice the cargo capacity. For the same animal or team pulling the cart or wagon, a cart typically has a higher cargo capacity. If the wagon has wheels the same size as the cart's wheels, the wagon is heavier, and has more losses due to friction. If the wagon has smaller wheels, it is less efficient, especially on rough terrain. The difference is not large, but as far as it goes, it is the cart that has the advantage.
Carts have another advantage: they have much smaller turning circles, and are therefore much better suited to urban environments. Wagons with pivoting front axles have smaller turning circles than wagons with fixed axles, but carts still have the advantage.
This combination of better cross-country performance and better maneuverability in urban environments mean that for most purposes, carts were preferred over wagons.
Wagons also have one important advantages over carts:
This often makes wagons better passenger vehicles than carts, especially when they are large. It can also make wagons better for very large and/or heavy loads. These are the two of the very old main uses of wagons: passengers and very heavy loads. This includes their use as mobile homes by steppe nomads, which often combined both passengers and heavy loads. The poor maneuverability mattered little on the steppe, where plenty of space was available for turning. There were other specialised uses for wagon where stability was important, such as mine cars. Wagons saw use as passenger vehicles from Roman times, and into the Medieval period, but Medieval use was largely limited to women as passengers, since riding a horse was proper masculine transport, and riding in a wagon was often regarded as quite unmanly.
Improved roads between cities/towns, and wider roads in cities/towns, and the pivoting front axle reduced the disadvantages of wagons relative to carts. In 16th century Europe, the 4-wheeled passenger carriage became acceptable for men, and the no-longer-emasculating wagon became much more widely used.
For more on wheels and their history, see