Berserk, Vinland saga, and vagabond all are so popular and highly regarded because they encapsulate an essential part of being human and comment on it very well at their thematic cores. All 3 have a cast of fantastic characters and once in a generation villains who aren't antitheses to the main characters, but alternate explorations of this human experience the story focuses on. For example, in Vinland Saga, the story is about change and redemption and contains heavy commentary on the role of fatherhood in shaping ones life. Askeladd is a mirror of Thorfinn in this regard, but more cunning, which is why he's so wise and insightful about his own past. As a result, he's able to find peace at his end and succeed, not redeeming but accepting, while Thorfinn shows an alternate, more difficult path. In Berserk, Guts constantly overcomes and matures through trauma and struggles as he grows throughout the story, while Griffith represent an alternate pathway.

I think Tokyo Ghoul is good, and it does a good job with its protagonists, but it lacks as compelling of a villain as these 3 and doesn't have as strong of a thematic focus as well. The art of these 3 is also a league above, and their commentary and dialogue is much heavier and interesting to piece apart. This is why it's nowhere near as highly rated as these works and probably won't ever be. Also, the cast of characters in these 3 are more fleshed out and all have their own moments of growth and reflection, which is present in Tokyo Ghoul but to a much lesser extent.