Are you referring to the fact that they are all in-house titles? Because if so, then you aren't expressing an understanding of the current market.
In the PSone era (and to an extent, the beginning of the PS2 era), there were few third-party publishers that localized JRPGs specifically. When you had hardcore games that were not properties of a major publisher come to market, they tended to be from Working Designs or Atlus. Enix published Enix games, Square published Square games, Capcom published Capcom games, and Konami published Konami games. There were one-offs, sure, like Midway publishing the first two Shadow Hearts games and SCEA publishing the first few Wild ARMs games.
The market is more crowded today. All of the aforementioned publishers still publish their own games. There are exceptions here, as well, like when Ubisoft published Drakengard 2, or when Nintendo publishes some of Square Enix's handheld games. However, when it comes to third-party localization, the field is more crowded. While Working Designs is obviously no longer around, the market has seen rise to XSEED, Aksys, Ignition, and NIS America in a space where there were fewer publishers competing for licenses. You are also seeing Japanese companies with US arms, now. Marvelous and LEVEL-5 both have offices in North America to focus on their titles. There are fewer quality third-party titles to go around, especially as development costs for PlayStation 3 and Xbox 360 titles have risen.
Atlus doesn't have the pick of the litter anymore when it comes to the games that they can localize. Dragon's Crown is Ignition's baby, Grand Knights History is XSEED's, Disgaea is NIS America's, Hoshigami Remix was Aksys'. These are all titles that are from developers that Atlus had previously published for. If your complaint is that they are localizing fewer third-party titles, you simply have to look at the market to see why that is true.