Just like restaurants, game centers come in three basic types: national chains, small chains, and independent stores.
The best-known game centers in Japan are run by major game publishers: Sega, Namco, and Taito. Their brands are established and they have the capital to stock the best goods. In addition, they periodically have fan events or campaigns. Sega is the largest of the three as far as I can tell. Their female employees are often avid cosplayers, and generally seen dressed as current-series characters while working. Since I’ve been back, they’ve been hosting frequent 500円 campaigns (spend 500円 in one go and you can collect minor prizes or points toward better prizes). These are the heavy-hitter places: they tend to be brighter and more colorful than their smaller counterparts because they have the most capital to spend, and carry all the major-brand prizes in high quantities. They’re also the place to go for kuji prizes, and high-dollar stores will often have more than one kit for each kuji.
I know of only two smaller chains: Adores [アドアーズ], which is fairly prevalent in Tokyo, but has almost no presence outside the city; and Leisure Land, which is spread very thinly across the country. Adores also sells kuji and periodically features cosplaying employees, while Leisure Land is pretty ordinary.
Far less famous (but no less ubiquitous) are the independent game centers. A few are small chains boasting two or three stores, while others are truly independent, with only a single location. These are the wild frontiers of gaming, with older machines, different rules for UFO catchers, and staff behavior ranging from helpful to indifferent. Prizewise, they tend to carry some of the current crop, but they frequently feature odd and useful things the big chains won’t stock and the smaller chains only occasionally do. (Examples: shock-staplers, Bluetooth gloves, off-brand handheld game systems, mini deep fryers). These places have more choice in what they carry and how they comport themselves, but more to lose if their product doesn’t move.
Interestingly, the location and visibility often up- or downgrades certain places. Smaller game centers in high-traffic areas like Akihabara will often have better stuff in stock, while big-name stores located outside major areas might resemble their small- or medium-sized peers (e.g. shabbier appearance, indie-style prizes).
So what does this all mean? It means that the larger game centers will have a better selection of popular-series prizes and video games. They’ll be more crowded, but will have a more attentive staff who will eventually make it easier for you to win a prize if you’ve hit a wall (because disappointed customers aren’t repeat customers). Meanwhile, the smaller game centers will vary in terms of prize selection and quality, difficulty of winning, number and helpfulness of employees, and how current their games are. Try ’em all, I say, and see which ones fit your skill and expectations.