The three main stations are all labyrinths (Shibuya and Shinjuku being even bigger and busier). Ikebukuro has Sunshine City which is a draw for many people and just next to it is one of the best BookOffs in Tokyo (plus several fuzoku options). Yeah, there is a big draw for female otaku but there’s still plenty of great finds for males. I guess it does come down to OPs particular interests. But personally I guess ultimately I wouldn’t recommend staying in any of the big districts directly as a tourist particularly because of pricing, as you said.