The scheme of "high speed rail with Amtrak regional for local service" was the original idea: HSR on I-5 with a Bakersfield station that allowed cross-platform with the San Joaquins. Perhaps a station west of Firebaugh with a cross-valley connection to Fresno and the San Joaquins. Otherwise, HSR was to be flyover traffic only (economically questionable if the idea was to even just break even on operating cost). And as far as Bay Area-Valley towns service was concerned, Amtrak would stay the same slow wanderer that it is now.

Things have changed. HSR now will replace Amtrak south of Fresno (or else, Amtrak will run on it), stopping only at Hwy 198 and maybe Wasco (is there supposed to be a station there?). Other places like Corcoran will be served by buses radiating from those stations, which may or may not be Amtrak or state-operated.

North of Fresno, it's easy to connect the constructed (under construction) HSR to BNSF for Amtrak to switch over (and perhaps priority freight, but let's not go there right now). Less easy (given how it's been built) to connect to UP even if UP were willing to accept it. Which means that full-length regional service (not just commuters) needs to stay on BNSF, which is faster than UP anyway (even now, at 79mph cruise vs. maybe 70 on UP). If everything were switched to UP (I'm just not seeing that being a happy negotiation), some kind of connecting track to BNSF or the HSR tracks would need to be built south of Merced. Even if the UP activity remains commuters only, if it goes as far as Merced, there will be a need to get over to the BNSF/HSR line for a cross-platform transfer. And sorry, I just don't see riding a ACE commuter train from Sacramento (note: no connection to the Amtrak station at Sacramento in current plans) to Merced to reach HSR or Amtrak as very attractive.