Great questions j.
The keys for any successful transit system are simple.
1. Well planned routes.
2. Frequent schedules.
3. Timely service.
4. Low operating costs.
The most difficult item in most systems is keeping costs under control. Salaries, benefits, pensions and staffing levels need to be reasonably managed.
In many cities the government owned transit authorities have become dumping grounds for politically connected no show jobs. In addition, arbitration laws in most US states assume rate increases and or tax hikes are reasonable sources of money for unions to justify pay raises, lavish benefits and enviable pensions.
Transit systems that have run operating deficits for decades are forced to give pay raises that outpace income increases in the dreaded private sector. All subsidized by taxpayers.
Bostons MBTA is a great case study for all of this.