Thinking more into this, the answer to a lot of gameplay issues actually would be to drop the number of VitaChambers (2 per level, maybe) and seriously drop the number of bad guys. Then enable bad guys to respawn at the VitaChambers too, unless caught by a little sister (and thus drained of adam). This opens up some nice avenues of gameplay, one it slows it down a lot to enable you to actually be tactical. It lowers the number of bad guys allowing for more distinct-ness in them. It makes little sister harvesting an interesting issue, do you kill them early to get adam or let them run around as cleanup crews for and then only kill them later.
Despite that dream which will never happen, one nice thing has happened. A patch for BioShock has been released and does support turning off VitaChambers completely. More details on the patch at http://www.2kgames.com/cultofrapture/pcpatch.html