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There's no reason why we have to wait for the intra-city transit to develop before developing the inter-city transit, though. Ideally they'd happen in parallel, with the inter-city rail fanning the flames of demand for robust intra-city mass transit.

And we should be clear here that "mass transit" within a city (especially one the size of Merced or Bakersfield) doesn't necessarily mean a full-blown metro network. Even a decently-sized bus system would be a step in the right direction (and in fact might be all that's practical or necessary for the smaller cities). On that note, both Merced and Bakersfield do already have bus networks, and the rail connection between the two would be a good way to spur further expansion.

The "two train stations to nowhere" are - from what I can gather - a temporary situation while we rejustify the rest of the network. Those stations are likely already in-progress and too late to cancel (probably because they were the easiest).