AP calcs are shockingly close here, and both characters are considered generously superior to the characters the calcs source, so this seems pretty close in power output.
Anna's got a lot of great options here, and can match Kakuzu in a lot of ways. Comparable intelligence and skill level, she's outranged but has abilities and gear to teleport farther than Kakuzu's attack range so she can kinda negate that advantage. She can reduce AND redirect incoming damage, negate durability, passively and actively heal herself, absorb energy from Kazuzu for healing herself, summon in help, manipulate both her own stats and lower Kakuzu's (as opposed to Kakuzu who can only increase his own), use poison, forced sleep, curses that affect stamina AND regen, one hit kill move, duplicating herself, electric attacks and weapons to target Kakuzu's main weakness, temporary invulnerability. The list just goes on and on with Anna, at first glance I think she'd soundly take this fight with all the ways she reduces how badly she's hurt, punishes anything Kakuzu does, heals herself, and just messes with him at every turn.
...Except for one problem. "Regenerationn (Low-Godly)"
How does Kakuzu access 'Edo Tensei'?
I'm not a fan of Naruto so I have no idea, but I'm pretty sure Anna has no answer to a Low-Godly Regen. Fire Emblem characters CAN fight and kill souls, but how that's applied in this situation is kinda unclear, which means despite all those advantages, Anna might not be able to put Kakuzu down.
Her sleep manipulation and poisons might be able to incap since he doesn't resist them, and it doesn't seem like he has a way to get past her BFR options with outrealm gates (Though, BFRing him might require some clever thinking, the lifting strength difference is huge so Anna's going to need to make use of powers and gear to actually get him in the portal), but that Low-Godly regen has me unsure if Anna would win this through battle alone, despite all these advantages I believe she has.
Anna's commanding the battlefield, so I still think she can win through alternate win-cons, but I'm doubtful she could kill Kakuzu, so a tentative vote for Anna.