I'm not sure if anybody noticed this, but the main characters (with the exception of Ainsworth, because she's English) all have last names that correlate to station names in Tokyo: SHIINAmachi station, KANDA station, AOYAMA-Itchome station, AKASAKA Station, KAMI-IGUSA station, MITAKA station, and SENGOKU station.
All of the other characters have corresponding station names which are serviced by trains that run into the Greater Tokyo region, if not into Tokyo Metropolis itself:
Himemiya (Saori's borther; Saori is the music producer for Misaki's anime) is a station on the Tobu Skytree Line, which runs into Asakusa;
Hase (the girl who moves in after Misaki and Jin) is a station on the Enoshima Electric Railway Line in Kamakura, which is in the Greater Tokyo region;
Miyahara (who has a crush on Nanami) and Takasaki (both of them being Sorata and Nanami's classmates) are stations on the Takasaki Line, which runs into Omiya (trains themselves run as far into Tokyo as Shinjuku/Ueno);
Tatebayashi (Student Council Prez and Jin's close friend) is a station on the Tobu Isesaki Line, which also runs as far as Asakusam although the kanji is a little different;
Nakano (original character from the visual novels) is a station on the Chuo Line, which runs mostly in Tokyo;
Shinagawa (also from the visual novels) is a hub serving many lines, including the Tokaido Shinkansen, which starts in Tokyo station itself. Shinagawa is in Tokyo, too, and;
Fujisawa (alumnus of Suiko) is a station on the Tokaido Main Line, which runs into Tokyo.
Shirayama and Iida are a bit trickier. Shirayama and Iida aren't anywhere near Tokyo, but just as there is no Shiina station, only Shiinamachi (Shiina Town), Iidabashi (Iida Bridge) station is smack right in the middle of Tokyo Metropolis, and the kanji for Shirayama (白山) can also be read as Hakusan. Hakusan station (with the same kanji) is in Tokyo.
The cats Sorata took in also carry significance: they are, or were once, Shinkansen services running on different Shinkansen lines--Hikari, Nozomi and Kodama on the Tokaido Shinkansen, Aoba (now obsolete) on the Tohoku Shinkansen, Asahi (now obsolete) on the Joetsu Shinkansen, Tsubasa on the Yamagata Shinkansen, and Komachi on the Akita Shinkansen.
Just a little trivia.