Takah: I agree with you. As someone who davvens on the bus ( I admit, I am lazy to get up and go to shul), I am appaled how little of Hilchos Teffilah people know. You do not need to stand when traveling, not even for Shemona Esrai!
You are correct, you probablly have more Kavana in those 30 minutes, then anyone on the bus because 1) getting up and down while the bus is moving, is not so easy, 2) constantly waiting (feels like 5 minutes) until the old man allows the Baal Tefilah to continue because we passed a landmark is distracting. 3) If you are one of the unfortunate people who has a seatmate, it is also cramped having a coat, tallis/teffilin bag and your belongings on top of you.
For anyone to disagree with the OP that we cordon off the women and keep as many seats as possible is lying and rishus. The FACT remains, the mechitza is usually up before women get on the bus and we determine where and how many seats they are allowed to have. Before the mechitza is moved to grant more space, we verify that they are all doubled up while the men have rows to themselves.
So before you argue or disagree with me, please show me ONE minyan bus that the mechitza goes up on the GSP when davvening starts.