Spend half my time in Tokyo; half in SFO. OP probably, but not definitely, wrong. I have been turned away from places even when dressed nicely. Usually outside Tokyo where the staff don't want to take on speaking English. Late at night, at certain high end bars, they only want regular customers. Brick Square is unlikely to be a location that turns away people. There are big money gaijin executives with influence there.

A poster mentioned calling the police. That poster is wrong. Discrimination is not a crime in Japan; it is unconstitutional but no laws were made about it so it is not illegal. So the police would do nothing other than laugh which is the reaction others have given me when I point out discrimination in Japan. There is a law about hotel discrimination but it is obviously not enforced as outside of Tokyo there is A LOT of that.

The OP seems clear they are not sweatpants and baseball hat with a nylon hiking jacket type of people so that is not likely it. In Japan cool, young people DO NOT get priority over older people. In Japan older people are higher status inherently in all things. So OP is likely not right about that. Remember that is why you see attractive young ladies with mellow older guys (the older guy is very high status) who are not always wealthy.

Joel Roubchon- Roppongi Hills location is pretty disappointing; the Ebisu location is quite good though. Try Cicada, or Elio. Restaurants in the Conrad or Mandarin Oriental are very good but VERY expensive.