Just one basic question - if Neo can stop bullets and jump into agents then why can’t he stop a sword he sees coming?

Sure, we see him stopping them with his hands and eventually getting nicked. I mean why doesn’t he just stop the object where it is at like he does with bullets? He’s not stopping time, he’s freezing an object at its current XYZT placement, so even if the upgraded agents and Marvy’s crew are not the same code Smith was, the objects themselves should still be the same unless the entire Matrix was changed… and if the entire Matrix can be changed, do they really need The One for the full reboot?