Based on my observation, these two companies cater for different audiences and they vary greatly in game presentation. It doesn't simply boil down to the preference of who you ask, it roots into more deeper levels and factors such as region, age, and other whatnots which are all interconnected to each other.
First and foremost, let's take the regional perspective as an example. When we say Square Enix the likely thing to pop out in the mind of a westerner is simply Final Fantasy or Kingdom Hearts. These games achieved gargantuan success globally and are both presented with cutting edge graphics and other whatnots that could be easily appreciated by almost any gamer.
Atlus on the other hand never really went neck in neck (it's a big and popular company tho) against Square Enix in terms of overall popularity in both western and global scales. During the past few years when the appreciation of the west towards anime escalated Atlus' popularity started to boom there as well. With it, a lot of Atlus games started to get noticed such as the ones mentioned earlier, the Shin Megami Tenseis and the Trauma Centers.
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In comes the age factor, most gamers which started to be pledged gamers during the latter game and console generations will MORE LIKELY prefer Square over Atlus. Simply because their very memory of the "great gaming era" are rooted to games such as FF7-FFX, Kingdom Hearts, Chrono Cross, Parasite Eve and other games which came out during the "graphical renaissance".
When asking someone who've started to "play earlier", it's really hard to predict the answer. Both parties have big guns to boast, Square has Chrono Trigger, the Dragon Quests, and some notable ones. Atlus can boast the Growlansers, the Megami Tenseis, Thousand Arms and other notable games during the "graphical renaissance" which managed (barely) to hold on to tradition.
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Closely related to the regional factor is the anime factor, like what i've said earlier Square's games could appeal to the general gaming populace. Square may be a Japanese company but their games are clearly less-Japanese compared to Atlus'.
With all the anime looking characters and traditionally animated cutscenes, Atlus games can be easily appreciated by the otaku fanbase and those with a degree of appreciation for the Japanese craft and way.
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Another factor that i would like to mention is gameplay. Both parties offer complex stories and other fancy things in between but both differ in their fortes. With a long line of big name RPGs, Square is more widely know for it. Their games are probably the-games-to-play in terms of RPGs. They have other great games outside the genre like Ehrgeiz (fighting), Brave fencer Musashi (action/rpg) and other Taito classics...but still, it's their RPGs that come to mind.
However, Atlus has it's own share of great games in all genres most notably in tactical games but they had weird and unusual elements in them like dating (thousand arms), rock n roll parodies (Guilty Gear)whatnots that might not be too appealing to everyone. Let's put it this way, with Atlus it is so usual to encounter the unusual.
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I could say that i've kept up with both companies' games for so many years, during the early nineties up to this very day. In my life as a gamer most of the games i've played hail from these two (err...four, taito, square and enix) companies. I could say that my preferences and appreciation is more in tune with Atlus since some of the best games i've played and my favorite game (ever(Brigandine the Legend of Forsena)) are Atlus natives. Square follows close tho...They're my first and second most favorite gaming companies anyway.


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