I've only played SS2 but here's my two cents.
Bioshock kinda lacks the exploratory nature of System Shock. Also lacking in how impactful customization along with much freedom in that regard.
Though System Shock was quite awful in some regards to this. There were utterly useless skills. You could completely lock yourself from progressing if you ran a complete butts build. At the same time IMO, Bioshock went completely too far in the opposite direction where it just kinda gives the impression that there's some customization and RPG gameplay elements, but is really just a linear shooter at its very core.
I'm also not sure how well balanced the Bioshock games are. I definitely exploited the hell out of the fact that I could respawn indefinitely from Vita Chambers. I had the vague feeling in BS1 that I might have been in lots of trouble if I had the Vita Chambers turned off. It didn't feel like I could really avoid getting damaged. BS2 and Infinite felt less bad in this regard, probably because of Plasmids and Weapons being separate rather than having to choose between the two which is armed, so combat felt more fluid.
Granted SS2 has janky ass combat as well and I mostly got past some more 'threatening' enemies through total bad AI exploitation cheese. I decided that smashing the combat robot to death with my laser rapier just led to me taking less damage overall from its death explosion, since it couldn't actually shoot me when I was stuck in its face between its guns. Trying to take it on in a gunfight however, would likely just lead to my demise.
Though I kinda find some charm in older jankier gameplay systems. Which while could completely ruin your progress, could also be exploited in the opposite direction to give you god like powers. I don't think I quite got to that stage in SS2 due to a corrupted save game ruining my run, but I quite enjoyed the absolute nonsense in Morrowind, Fallout 2 and Deus Ex. It felt great when I figured out I could just turn on my leg augs in the Vandenberg Air Force Base, leap off the helipad and destroy all four robots as I landed with my Expert heavy weapons skill.