I find women who choose to sit next to another woman on the bus, when the bus still has lots of sitting available, are probably experiencing mild form of social anxiety. That way they can control who they sit with and are not stuck sitting next to a strange guy, for the duration of the trip to wherever they are going.
Not everyone is as confident going out and travelling alone or even just commuting to work. Even the ones that argue about you removing your bags so that they can sit there, are showing just how desperate their need to control their environment is. If you find them a little too much just smile and stand and say please be my guest, when they settle down, then just move to another seat and continue to enjoy your commute home/to work.