Going by sales, Pokemon and Mario win. But going by Popularity...there's a question to which would win. You have to remember, there's still less games in the Dragon Quest series than Mario and even Pokemon, even with Dragon Quest come out some 10 years before it (and influencing it greatly).
There could be an argument made that Dragon Quest takes more time (and puts more quality) into making its games than some other series, even Pokemon. And, while I'm a fan of both Pokemon and Dragon Quest, I'd say Pokemon has been a series divided, with one 'main' series and a number of spin-offs of varying quality and range of sales. Whereas Dragon Quest has been a rather stable series with every game getting a large amount of attention put to it, because the same 'core' team works on all the games (even the spin-offs).
Ultimately, the argument comes down to popularity however. And I don't know if that question can be answered. In terms of sales, Pokemon definitely wins. But in terms of popularity...I'd have to say Dragon Quest still wins simply because when a Pokemon game comes out, other games still sell around it. When a Dragon Quest game comes out, the nation shuts DOWN and other companies clear their schedules for 3-6 months (okay, exaggeration, but Japan really does see an impact).
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