Eliza is without any doubt the strongest of the playable characters, guess that's hardly surprising when you make what was meant to be the boss of a game a playable character ^^'
There is very little competition for her as her blood powers are just hacks. As long as there is enough blood, she can overpower any enemy.
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Assuming she does not have all the blood she needs though... I am somewhat hesitant about this one, but I'll go with Double. She rarely fights to her full potential, but I believe when she does she overpowers the rest of the cast.
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Now interesting case can be made for Painwheel and Peacock - in that order. Who are fairly weak at this point in time, but have potential to be incredibly powerful when their powers are harnessed to the fullest.
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Under the two of them we have the Theon hosts, aka Squigly and Filia, the power of their parasites carries them above the normal humans, though it is a bit unfair for Filia, as Squigly, when she wakes, is being powered by the Skullheart, but overall her skillset is far more versatile, and being undead makes her a lot more durable.
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Next in his own category we have Bigband, who is an ASG soldier, surpassing human limits, but without any latent potential or powerups.
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And we reach the bottom of the list which are all the humans, Valentine with her combat experience and genetic modifications, Cerebella aiding herself with Viceversa, Nadia Forune being heavy carried by the life gem, then Parasoul and finally the man himself Beowulf
Can not place Annie until I play her story mode, but I very much expect her to be near the top of the list.