Well at this point it's just a major stomp for Jensen. He's got armor that makes him completely damageproof. A 360 degree explosive attack. Superheated, magnetically launched arm blades. Taser shots. He could just hack her. Etc... He's got so many powers now it's crazy.
Yeah. He's got every power from the first game. Then you discover after the end of the first game, that the whole time he was unconscious, people were putting in illegal, bleeding edge and highly experimental mods into his body.
At this point, with no in-game mechanics, Jensen is a tank that can turn invisible, shoot superheated nanoblades with enough force to pin people to walls, has his Typhoon, etc, etc, etc...
You're going to have to be more specific with stats, because Motoko Kusanagi is fast enough to avoid gunshots from weapons from a setting that is frankly more advanced than Jensen's, strong enough to keep a helicopter from taking off with her bare hands, durable enough to be virtually immune to small arms fire, and is a potent enough hacker that when she agreed to spar with Bato she easily hacked into his cyberbrain and forced him to punch himself in the face, without so much as a change in expression from her.
Check 2:25. Can Jensen match this feat, or exceed it, with one of his own?
At 1:55 as she fights the mech we see her avoid its fully automatic gunfire, and later on survive it literally stomping on her head through concrete.
At 1:17 we see Kuze leap through the roof of the building, then hundreds of meters through the air. This is notable because both are cyborgs, and as we see Motoko could match his strength earlier while protecting the Japanese Prime Minister.
Shitty Green Day AMV, but good feats here. Ten seconds in, could Jensen match that level of agility?
At 3:41 we see her replicate Kuze's feat of leaping hundreds of feet, and right after (though they aren't the same scene) land with enough force to crater the ground, though the latter feat was in the opening so I don't know if you're willing to accept that.
The hacking feat in question I mentioned earlier.
At 1:45 we see her literally shoot a sniper bullet out of the air.
Jensen's definitely got the edge on her in terms of weaponry. Between his nanoblades, tazer, typhoon and pulse-cannon. And guns of course. He can also do a short-range teleport (think Dishonored) and with Titan he's (afaik) immune to bullets, which the Major isn't.
He can also perform remote hacking, but I doubt he'd do shit to her that way.
I'd say that if the trailer for Mankind Divided is accurate about his abilities, he'd win.