Will's connection to the Mind Flayer lasted into season 3 and has now been shown in the fourth season of the show. Will is still connected to the Upside Down, with his time there and the particles of the dimension that entered him acting as a sort of anchor that keeps bringing him back into the realm. The fact that Will senses something and the whole crew runs to see the Upside Down suggests that what started with Will in season 1 might end with him in season 5.
The Mind Flayer and the rest of the Upside Down have been led by Vecna since the beginning of the show. The opportunity to give Will the spotlight the character has deserved for so long and use him to fill a valuable role in the struggle against Vecna is not going to be missed. Vecna's access to monsters and superior numbers doesn't bode well for the main cast, so having Will's help to spy on the villain's plans might be the only way to beat him. Will either gained a connection to the realm or was granted a connection to Vecna in a way not yet fully established while trapped in the Upside Down.
The Mind Flayer was able to enter Will's body and use him as a host in the second season of Stranger Things. Exploring the new world he's become trapped in, one encounters the Hive Mind particles and bends them to his will, connecting himself to the realm and becoming its master. Due to his status as being stuck in the Upside Down, he's a major focus in season 1, but he's barely in the show. Will's connection to Vecna is one of the few edges the Hawkins crew have on Vecna that the villain doesn't have any control over.
The main cast's struggle to kill Vecna and close the Upside Down off from the real world will be the focus of the fifth season. He runs, ends up in the Upside Down, and hides for the better part of the season before being rescued. It's being set up to change how it has handled Will's character because of his connection to Vecna.
Will is connected to Vecna, but not the Hive Mind, meaning he isn't hurt when other parts of the Upside Down are.
Knowledge is power, and having a character who might be able to act as a spy against Vecna and his forces may tip the battle in favor of the Hawkins crew. Will's connection to Vecna will be important in the fifth season of Stranger Things. In comparison, Will's character is used more and gives him some powerful moments, but he's still in the background. Will was riding his bike home when he was stopped by a Demogorgon on the way to the hunt. Season 3 uses him relatively less still, abandoning a storyline about him feeling neglected by his friends in favor of the rising action of the season.
The connection between Vecna and Will was revealed in the second volume of the show. Will being taken in the first season of Stranger Things may prove to be Vecna's forgotten problem.
Since the very first episode of Stranger Things, Will and the Upside Down have been connected. This connection may prove to be Vecna's undoing, as it gives the team insight into his plans and a heads-up before he acts.
Will doesn't get a lot of time in the series' first four seasons.