Eidos was founded in 1990 and has been the king of its own destiny since its inception. As part of Square-Enix, Eidos and its destiny were called into question, would they continue to run the show or would they become one with Square-Enix. Square-Enix has come out to say they’ll be leaving Eidos to themselves and allow creativity to flow between the companies.
“This is an exciting beginning to what I believe will be an incredible journey. I am very happy that Phil Rogers has agreed to lead Eidos in what I see as an international marriage between our two companies, a marriage that will give birth to great things. Eidos is a content rich company and a culturally significant business to the Square Enix group.” (kotaku)
Square-Enix is playing it safe with this acquisition because this isn’t a great enviroment for shaking things up internally within a development studio. Eidos is well known for Tomb Raider, Hitman, Deus Ex, Thief and many other great projects and have built a solid foundation for the future.
A mind-share between these two groups is a powerful enemy to the competitors if they’re able to open a good dialog between the two companies and share resources, tools and engines. In a world of cost savings and salary cuts, leaning on each others resources to build a better product is a win.
At least we won’t have to call them Square-Enix-Edios because that’s just a mouthful!
The Xbox 360 saw a 
“Questing.”
Square’s Yoichi Wada has just said in an interview that Japanese game development is “almost xenophobic” and that Japan is falling behind in game development because they’re too insular:
http://www.developmag.com/news/31756/Square-Japans-game-industry-almost-xenophobic