I'll bump this with an updated analysis.
So without shields it does improve Jensen's odds in frontline combat. But not enough for me to say Jensen would win in a straight fight. Even without shields, Shepard has superior armor, weapons and training.
Both their AP are marked at small building level. Shepard has been scaled to the Shadowbroker. Jensen's been scaled to his augments.
So I should've been more detailed regarding the smoke grenades. If Jensen throws a gas grenade, as long as Shepard as a helmet, nothing will happen. Jensen could throw them to the end of time and nothing will happen. It's a hard counter. Shepard doesn't have a hard counter to smoke. No thermal or sonic vision to render it useless. And Cerberus troops wouldn't use them if they didn't have their uses.
But smoke won't be a guaranteed win. But they're like the grenades as they at least help increase the possibility. If Shepard stands in the smoke, he has to accept loss of vision and Jensen can take advantage of that. If he runs, Jensen can herd him. So no promises but it does open more avenues. Of course Shepard also has to behave how Jensen wants and no doubt N7 training will cover smoke cover. So it's like the grenades. Shepard can get out of range of normal grenades but he doesn't have a point defense system to just neutralize them. Smoke grenades won't guarantee Jensen a win since it's one thing to surround Shepard in smoke and it's another thing to capitalize on it. Not guaranteed but it still helps Jensen since Shepard can't nullify it.
Now regarding battlefield awareness software. What if Shepard does have a minimap like we see in ME1. This is huge to the point I'd have to rethink Jensen's victory as it effectively means Jensen can only use stealth if he cloaks. He isn't like other stealth characters like Corvo Attano who could be leaping across ceiling rafters. If the minimap pings him ahead, he's hiding ahead. The most that Jensen could do is hide on an upper floor and have Shepard thing he's on a lower one but that's it and that's not much of an advantage.
But as mentioned, I don't think it works that way. And we can see this in several moments regarding characters like Thane. While tailing Kolyat, Thane vanishes into the crowd and Shepard doesn't know where he is. Likewise, in Thane's recruitment mission. They couldn't just use tech to locate Thane. They had to get to Nassana first. And when Thane fell from the ceiling, he caught them off guard. We also see this with Kai Leng. When Kai Leng tries to assassinate the salaran councilor, he was within line of sight and Shepard doesn't notice him until he looks right at the guy. Likewise Kai Leng doesn't notice Than sneaking up on him. And While Leng isn't Shepard, they should have comparable combat awareness software. Another one is when they were talking to the prothean artifact on Thessia. It was the artifact that alerts Shepard and crew that Leng has walked in.
While Kai Leng does fail to sneak up behind Shepard, he was already on the brink of death. So I don't think this indicates Shepard has some sort of inherent ability to detect sneaky enemies. He does have good awareness overall. I forget which scene this was. But him and his squad walk into a room and there was a civie hiding behind some boxes. Shepard does sense that there is someone there and calls for them to come out. Namely announcing "Company" then drawing his gun and aiming it in the civie's direction. So perhaps anyone that isn't a stealth master would be detected. And this actaully rather lines up well. He would notice anyone that isn't an expert at hiding. And while Kai Leng is, at that moment in ME3 he was fatally wounded and not up to par.
Now let's open up the awareness software to more interpretation. Let's say it's proximity software. With the exception of Thane sneaking up on Leng, the sneakers were a distance away from the snuck up on. So let's say that Shepard won't get alerted unless Jensen gets close. While this does shift things slightly toward Shepard's favor I don't think it'll net him the win. It means if Jensen wants his stealth kill he'll need to go in cloaked. It also doesn't negate hit and run attacks.
I should also add that Jensen matching Shepard in melee combat requires his Titan. Shepard is better trained than Jensen. Sure dual wielding does have an inherent advantage over a single omni blade but I think N7 training is advanced enough to say Shepard still takes the edge. Jensen needs Titan to cover for any failings if he wants to match. If Jensen opts not to use Titan or doesn't have the energy, Shepard will easily win hand to hand.
Things like medi gel also solidfy my position. In a firefight even if Jensen manages to actually injure Shepard, Shepard can use medigel to patch himself up. Though Jensen does have passive healing. Then again, I'm still of the position that Shepard's weapons are superior so Jensen might not even get the chance to use passive healing.
There's also that Immunity doesn't protect against electrical attacks like Husk shockwaves. And Jensen has his TESLA augment which lets him shoot electricity.
So most fields do favor Shepard such as open combat and hand to hand. The one field Jensen has an edge over Shepard is stealth and it's a field Jensen is most likely to go to.
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