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!
After four years of development, 
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