The kids use Dungeons & Dragons (D&D) terminology to classify the upside-down monsters. In D&D, mind flayers (illithids) are a race of creatures feared around the world for their psionic abilities (via SkullSplitterDice). Also known as “mind lords,” they wield a variety of mind-affecting spells that allow them to control others. Mind-Flayers are even able to discern the thoughts and feelings of others, allowing them to tailor their tactics to each individual. They even look like squid-faced monsters, mimicking The Mind Flayer’s design in Stranger Things.
While Mind Flayers referred to an entire race of creatures, Vecna was a single character in D&D (via Dicebreaker). He began as a human and lich king who rose to deity. Vecna is considered a minor deity, capable of powerful magic and immune to many forms of damage, including mind control.
With all the information available about their D&D counterparts, there’s still a case for being one of the ultimate villains. However, Vecna did not exist until Henry fell into the Upside Down. The Mind Flayer, on the other hand, existed long before that, so the theory that The Mind Flayer influenced Henry since childhood feels more realistic.
Let’s not forget that Dustin also credited Vecna as a 5-star General for The Mind Flayer. They didn’t have all the information about Vecna at the time, but this quote could still point to who is actually in control.