Your first point is very true even in areas in the US with a sizeable Japanese and other Asian population like San Francisco and San Jose. The great sushi places in the SF area are small, hidden places and very expensive. In Tokyo, even the sushi-boat places (kaiten zushi) have generally good quality seafood at a value price.

Your second point is true and but it may be a little difficult to detect the chef's reluctance to serve certain items unless one is accustomed to Japanese (or various Asian countries') politeness. If one detects a slight hesitation or grimace, or even an inspecting glance at the inventory when one asks for a certain item, it might be that the chef doesn't really want to serve that item, and one would be advised to wave the request away and ask for something else or let the chef decide.

To the OP's question about tuna. Maybe you heard about the fresh, raw tuna used for sushi and sashimi and not canned tuna? You don't need to spend $200 for awesome sushi in Tokyo. You do however might have to wait in line. The good (to great) places have very reasonable prices (Y3500-4000 for a deluxe set) and the lines will be long. Off the top of my head, I'm thinking of places like Sushi Dai, Daiwa, or Bun in Tsukiji.