It's fairly linear though, I would have expected it to have more meaningful choices, but you don't have many chances to influence the plot.
But at least you have many options how to play (even though stealth is probably easiest).
I am also playing Deus Ex with GMDX mod, now in Paris which I presume is already getting closer to end.
It appears to me that the "story choices" are mostly some small side-plots, or if you change something related to the main characters, it still doesn't make a major shift to the main plot. To me that is quite ok.
For instance, I wasn't able to save my brother's life, but apparently in a big picture that just changes some future discussions where your brother is not present anymore and some give their condolences to your for your brother, but it is not like you go to some completely different areas or anything.
Or similarly, you are able to kill some of the main baddies earlier on, which just means they won't be taunting you in some later part of the game and fighting you there.
Then there was e.g. the small side plot related to the hotel owning father and his prostitute daughter. I guess you can neglect them completely, or alternatively try to get them back together. Maybe you get some extra experience points for that, not sure.
My gaming style seems to be mostly semi-stealthy where I do try to take all enemies down if I can, but by knocking them out from behind or with the stun rod if I can, just so that I can save bullets. But, if I sometimes feel that is too hard or time-consuming, I just start shooting around with my silenced sniper rilfe. One unscoped shot to head kills all humans, it seems to be the ultimate weapon against non-robots. Robots I usually try to avoid unless I have lots ot EMP grenades or other explosives, but I usually save explosives for opening some doors that would otherwise eat too many picklocks or can't be destroyed with the dragon sword or the sniper rifle.
Paris is now a bit problematic though, friendly policemen seem to become hostile too if I start taking down enemies... So I guess this is the first time I quite often try to completely avoid confrontation, even if I guess I could just kill all the policemen too...
I was under the impression that the assault rifle would in the end the ultimate weapon against human enemies, but it just eats too much bullets. If I start using it in firefights, I am always out of bullets in no time. The sniper rilfe is better, one bullet per enemy, even in close quarters.