Your rant is based on a sample size of one trip on one route on one particular day. Do you know how the trip(s) ahead of and behind you did? What about the other Connexion routes from Kanata? Or the rest of the city?
When the express network and fare existed, do you know how often I've stopped at these "irrelevant" stations? Despite the express fare, some people would still use the network at these stations. An express pass holder might need a different station that day, or it was someone who worked at the Queensway-Carleton Hospital, in Westboro, or wherever who did not want to make a second transfer to get home. Did you observe if the people who wanted off at those "irrelevant" stations were from the suburban local portion of the route or not? When the express network existed, a person could hail an express bus from any station in the afternoon. Some people also paid the express fare due to ignorance, mostly when the Presto ePurse came about, or due to the perceived inconvenience of stepping off the bus and waiting again.
Your proposed solutions are not "easy." Pinecrest has no off-only stop, because of its location immediately following a sharp curve. Dominion was never meant to exist, as that was supposed to be a temporary alignment of a Transitway that never got built. Extending the platform there would require some rock blasting. Implementing (or re-implementing, in this case) a fare class or removing service is not a simple flip of the switch.