There's nothing wrong with food-heavy cities being somewhat devalued. An easy fix, which you mentioned, is adjusting city placement. That's just part of the game. So is controlling pop, as Bite can tell you with much unhappiness. Food heavy cities can also be helped by ITR's. And bottom line, you aren't entitled yo have specialists in every city — you're just used to it. So was I, but I'm enjoying the new limitations.