I'm not sure what "soulful" actually means in this case, it sounds like a vague / handwavy term. Art direction? Style? Feel? Atmosphere? I'd like to refute the claim by posting some of my favorite (3d) games but without understanding I can't lol
It doesn’t make sense to want to refute an argument you don’t understand. If you don’t know what the argument means, you don’t know if you agree or not.
Seems like you’re assuming (probably correctly) that “soulful” means something positive in some specific axis and your immediate reaction is that no, the thing you like must be better in every way. That response is already tainted with bias.
3D (up to when I could be attentive) was immensely ugly, unartistic, if you take "2D as design" as a parameter. Flat (paradoxically), random - you take a screenshot and typically find the opposite of aesthetic pleasure. The instrument is not immediately fit for artistic purpose.
-- That more control can be imposed to painted flat material is hardly controvertible.
-- That the results prove that triangles defined objects are tools that require much higher mastery - well, if you cannot see it for yourself, suppose a panel of art critics will be there.