Why doesn't anyone use the substitution jutsu later in Naruto?
The substitution jutsu is still used constantly, but as the series progressed and the strength of the characters increased it became more practical to use clones instead as clones serve the same purpose and more.

There are notable examples of the substitution jutsu at the end of the series.


Kakashi using it against Obito in their final fight
Killer Bee uses it with one of Hachi's tentacles against Sasuke in their first fight


The technique is indeed extremely useful, and must be easy to do and require low chakra as it is taught in the Academy. It is likely a staple, fundamental technique that is used more often than we see, and is used so frequently and has such a low impact on high level fights that we likely forget if and when it is used.