I enjoyed the combat/quest balance of Mass Effect, especially as I leveled up my powers, but it did get a little combat heavy towards the end as all Bioware games tend to.
I totally agree with your opinion on Bioshock. The splicer combat got old after the first area, and not much new was introduced. The Big Daddy combat was fantastic. I think Rapture should have had significantly less splicers, and added pockets of survivors who were actually normal. These people could send you out on quests into the crazy parts, instead of you randomly just wandering around. This structure was handled really well in Ultima Underworld, and is pretty much the system used by all the western RPGs now.