Quasi-vampire Shinobu does not have mind manip, only her human key does.
The sword does not have regen nullification, but it inflicts death with a mere scratch. Regeneration doesn't let you come back from death manip. At least, anything below godly regen wouldn't.
It's a bit tough to tell what Shinobu would start with. In 3 of her fights she already knew she'd stomp them, so she waited until the instant Koyomi would have died without her help, then held them down to suck their blood, which worked. 3 of her fights happened completely off-screen. And in one of her fights, where she tried killing her 6-B/5-B key from another timeline, she created multiple copies of her death sword.
And fwiw, the only fights we saw from her in her 6-B/5-B key she was purposefully trying to lose, so not much help there either.
Still, she has handed out the sword to others who were about to fight, and shown it off from time to time. And there is the part of her backstory where she used the sword so much the sword's nickname (aberration slayer) became her nickname, so she's probably pretty willing to use it.
While Dio can dodge it, she can create multiple copies of it, and throw it with impressive accuracy. She can also dodge Dio's abilities, with the added maneuverability of hiding in shadows.
Better Hax, regen, intelligence, and experience
Sure he has better hax, but it's all on-touch, projectile-based, or OOC. Better regen, but Shinobu's main wincon here bypasses regen. Better intelligence? Definitely. More experience? Almost certainly not. Shinobu's been a vampire for 600 years, and been hunted by vampire hunters that entire time, she also commonly killed other supernatural beings to feed on during that time. No clue how you could say that Part 1 Dio's experience remotely compares.