Good game!
Well, I really liked the game, but there are a few things I'd like to see, which of course, since you asked for it, I'll gladly supply.
Are You Saying I Can Dodge Bullets?- I understand that bullettime is overdone, but a Matrix game without bullettime is like icecream without the cone... You could make the enemy stronger, to compensate?
Rooftop o' Doom - Really, I understand that agents are supposed to be tough, but you throw one from the top of a 13 story building, its going to be unlucky for them to land. To balance, falling from the top could be very painful for the main character (like 20 health or so?), unless you fall on top of an agent, in which case the damage is reduced (like 5 or so). Then, make the enemy, who normally jump off the roof to join you in battle, suicide agents who risk their "lives" to try to squish you underneath.
House Built on the Rock - Tougher floors, weaker walls. With the 'damage from falling' mentioned above, the player would earn the advantage.
I Am the One - More melee options, possibly to coincide with aforementioned bullettime, including a powerthrow which is essentially a combo throw and run that slams the enemy forward, and maybe an uppercut (to raise the roof) and a dropkick (to take them down a notch.)
And, finally, the ability to throw away all weapons, not just throwing weapons. If you don't want that handgun, throw it over the side of the roof.
Oh yeah, and a rocket launcher that is only available if you enter a cheatcode. =D