I ride BART several times a week, and completely agree its current state is parlous. However a few factoids (some dredged up from memory as they pre-date the modern internet):
1) Indian Gauge: I have heard the motivation was primarily stability in the event of a major earthquake occurring during e.g. rush hour
2) antiquated controller system: at least one attempt was made to upgrade it, during the 80's. One of the companies was a software contractor Logica (sp?). It was a classic large-systems cluster: over budget, late, never worked, subsequent litigation. I believe the original system used Westinghouse computers and at one time the number of trains during peak hours was limited by RAM exhaustion (measured in KB IIRC, might have still been magnetic core that far back)
3) the current problems have surfaced in part because they waited too long to replace the fleet; new cars not showing up until 2017 and they really were needed a year or two ago.
4) Aside from lack of maintenance (very real), a good argument can be made CapEx has been misdirected. Some alternatives to going south of Fremont that would have been more useful: removing SPOF at Oakland Wye; going out Geary (allegedly the busiest transit corridor in USA without rail); crossing the bay roughly where Dumbarton Bridge is. Alas the funding model for BART (and various intra- and inter-county rivalries) make all these political non-starters.
5) could be worse... consider any sprawly sunbelt city.