Not sure what comparisons would be fair. Our normal place isn't omakase-specific and by this point, we've been going there so long that we occasionally get some special treatment so I'm going to disregard that one.
Quality of the fish all over, to me, seems better now than even like ten years ago. It is very rare to have a clunker, might be variance, I dunno.
I think the closest comp to a place that I've actually been to is Hinata, and I think Hinata was slightly better value than Kabuto (if you don't factor in the expense of my car getting broken into while we were eating lol). SF places are likely superior for the diner right now due to the competition.
All things considered, I would take the two meals at Kabuto for the $$$ of one meal at Yoshizumi in San Mateo