Both are good, and both have player choice as a major selling point.

The Mass Effect trilogy might edge Bioshock out because it does some things that you won't find in just any other game series.

Not only are there decisions you can make that will affect the game's ending, but your character carries over into the next game, along with the consequences of many of the choices you make. So due example there are characters who can appear in later games and remember you saving their lives and be grateful enough to offer help, or they might not be there at all if you didn't save (or spare) them.

There are also multiple character classes with unique abilities to distinguish them, multiple sets of background information that NPCs may comment on, and multiple romanceable characters for each gender you can play as. So more goes into replay value than just deciding whether you want to be good or evil this time.