What a legendary battle!
What can i say about this...
Berserk: captures raw and unadulterated emotions better
Vagabond: captures empathy and melancholic emotions better
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Berserk: captures bloody and monstrous fights better
Vagabond: captures character-centric and iideologically-themed fights better
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Berserk: the art is primal, rough and explosive
Vagabond: the art is poetry, heart-rending and masterful
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Dragging factor: Vagabond wins. Berserk drags quite a bit. Vagabond doesn't do drag. It sticks to the key points it wants to make.
Twist factor: Berserk wins with its Eclipse arc, the greatest manga arc ever written.
Originality in concept: Berserk wins. Its a pure fantasy made from scratch, while Vagabond has a clear blueprint.
Main characters: Griffith wins. But Musashi, Kojiro, Inshun, Yoshioka Seijuro, Yagyu Sekisushai also win. It may be caused partially by nostalgia and endearment from us readers who wanted to see Musashi and his lore inserted in the form of manga. To compare those characters in opposition is extremely difficult.
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Conclusion: HOW THE FLYING FUCK CAN I MAKE A CONCLUSION ITS VAGABOND AND BERSERK FOR CRICKET'S SAKE!