- Broken Base: The reaction to Sega's acquisition of Atlus' former holding company has been mixed, with many fearing Sega's reluctance to localize games will affect future titles while others remain hopeful for the best.
- The western developed titles Atlus USA occasionally publishes tend to be disliked by it's core fanbase. While this is understandable for games of rather dubious quality they've published (Daylight , God Mode, the R.I.P.D. tie-in game (which itself is a reskinned version of God Mode), ACE Team's games tend to be thrown under the bus too.
- The constant Persona games, particularly those that aren't JRPGs. Some consider them to be good games in their own right, and encourage people to try out new (and less popular) genres, while others consider them to be little more than cash grabs that distract Atlus from working on other titles.
- "Atlus tax", or Atlus charging $10 more for games than compared to every non-Atlus game on what they're releasing it on. While it does have a limited edition (if there were only limited edition copies) feel to the first release versions, many, many fans are upset that the company is charging extra money for games that won't go down to the normal price after release, then releasing a large amount of paid DLC that screams "intentionally cut content". It doesn't help that they used to give out a respectable amount of the pre-order goodies for free before they started this practice.
- The decrease in difficulty and addition of convenient features in more recent Atlus games, such as the Easier Than Easy modes of Persona 3 Portable and Persona 4 Golden as well as Charon's revival services and the removal of Save Game Limits in Shin Megami Tensei IV. Some players cry "Atlus games are supposed to be hard!", others argue "If it gets me and my friends into Atlus games, so be it (and many of these features can be disabled anyway)."
- Cult Classic: Some of their games/series have very devoted fanbases. Although the description notes they don't have as much name recognition as other big companies, they are hardly unknown.
- Harsher in Hindsight: Despite the many jokes at the company's expense for its overhaul on Persona 3 and Persona 4, it was revealed that the company was starting to go bankrupt and needed to rely on its two biggest sellers in order to keep making games.
- They Just Didn't Care: Most of their games after Sega bought them have been of...significantly lower quality in comparison to their Index days, either in regards to gameplay, translation, or both.
- Woolseyism: As Atlus USA doesn't develop anything itself, most of its publishing involves localizing Japanese games, which it does quite well.