At the start of the series, every spammed substitution jutsu every five minutes, then why later in the series no one uses it anymore. Same goes for the function of the sharingan, it was shown as something that could easily see through other jutsus and then it's no more used for that purpose.
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1All though not a direct answer to your question, it does seem related. Why doesn't Kakashi use his copy cat ability that often?– Dimitri mx ♦Commented Jan 24, 2019 at 13:37
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2 Answers
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.
It ends up becoming useless, as the enemies evolve in anime many techniques can become irrelevant or ineffective. In the case of the substitution jutsu it becomes easily counter-able by enemies like Pain and Madara. Although in some cases it is still used in the place of a counter attack
