Sorry, any public transport system that relies on buses as the backbone will be a "shit show". Buses are uncomfortable, slow, unreliable, get stuck in traffic, etc etc. "Bus rapid transit", dedicated lanes and so on ease the pain a bit, but at the end of day, they just can't compete with any service that has fully dedicated right of way.
Unless you've dug a subway, how do you get people to the rail lines? Park and rides? All that does is encourage suburban sprawl to drive to a rail station.
There's no reason for buses to be uncomfortable and unreliable beyond popular perception. I've ridden trains in Dallas that have worse onboard conditions than bus routes in Seattle.
You do what everybody outside the US does: build housing within easy walking/cycling distance of the stations.
And it's a simple matter of right of way, not "popular perception". A train runs on its own tracks, so it can be scheduled to the second and stops only when needed. A bus shares the road with other traffic, and is thus subject to traffic jams, traffic lights, other cars driving crazily and breaking down, nutcases running across the road and so on, which means lots of unnecessary stop-and-go (compared to a train) and a chronic inability to stick to a schedule.
Yes. There are still many places the subway doesn't go. The buses are also crowded, and sometimes you have to wait in line for a couple of hours even to get on (especially to/from the suburbs). Of course, you might have to wait for 30 minutes to get on the subway during rush hour (e.g. finding enough space to fit in to an open car).
My only point here is that everything is quite relative (i.e. first world vs. third world problems).
As for bus rapid transit, I found the new West Seattle service to be quite fast and efficient (although West Seattle was already pretty accessible before).
