Because we have tons of ground-level sensors, but not a lot in the upper layers of the atmosphere, I think?

Why is this important? Weather processes are usually modelled as a set of differential equations, and you want to know the border conditions in order to solve them and obtain the state of the entire atmosphere. The atmosphere has two boundaries: the lower, which is the planet’s surface, and the upper, which is where the atmosphere ends. And since we don’t seem to have a lot of data from the upper layers, it reduces the quality of all predictions.