VTA serves Santa Clara County and the station is in Alameda County; and the next BART station will connect with VTA's light rail and be next to a large transportation center.
They have inter county busses, just see Fremont BART.
Sure, but given they are already planning on making massive changes to the bus schedule as well as light rail, might as well wait for BART to be in Milpitas before doing that, since it's supposed to be "this year".