They are the gambling machines, and almost everyone I know has a negative impression of them. The other type is well, the pachinko and slot machines shops/arcades. I will admit that atleast one Taito Station in the Tokyo suburbs has the smoking smell in it, but otherwise they are pretty nice places. The main focus is on fighting games, arcade games (well duh), rhythm games(like Ongeki, maimai Deluxe which I love), Densha de Go! (a realistic train driving simulator with the inside looking like a cockpit of a commuter railway train), some robot games, Dance Dance Revolution, Kantai Collection, Fate/Grand Order, zombie shooters and many more. It does have some machines that use 'medals', which I assume is some sort of gambling thing, but it's just a small subset. FYI, if the place you went to is a SEGA or a Taito Station, then it's very likely a game center. From my experience, there are two 'types' of arcades in Japan: one called 'game centers' (ゲーセン, pronounced gay-sen), and another 'pachinko' or 'slot', also called パチスロ(pachisuro).
