I think Wyll biggest issue was that he was the last companion people encountered most of the time. In the moment you can recruit him, you already have encountered Shadowheart, Astarion and Laezel so the party is most likely full. His introduction was also pretty bad I think. Him appearing without context or cinematic in a battle unrelated to the tadpole made people believe he is just another common npc.
This is also a good point.
If he hadn't been in the promotional material I wouldn't have assumed he was a companion until he offered to join the party. He didn't really stand out where he was placed and with what he was doing - which as I recall was training kids or something.
