Thanks Drek, and this will be my last attempt to shed light on this whole subject, hopefully I'm not as ignored as before. I do not know much about games anymore, but I was OBSESSED with Square back in the day, and I followed nothing more closely a decade ago than this merger.
First off: THE MERGER DID NOT SAVE SQUARE, NOR WAS IT REQUIRED TO. Everyone in this thread thinking/saying this, stop it. You are wrong. You are not right. Stop it.
Enix had a problem. They were essentially a tiny, completely unproductive publisher except for one mega-ultimate franchise. The problem? They controlled absolutely zero part of it. DQ is Horri's, and Enix could never control how and when he made them. Thus, the expansion potential of Enix was completely limited. But they were the definition of stable.
So in 2000, off the heels of the megaton explosion of awesome that Square experienced in the previous 3 years, Enix approached them to merge. But Square was hesitant, because it would require a larger share to Enix on the backs of just their one franchise, a franchise they felt they could eclipse in the coming years.
So they bickered and went back and forth as mergers do for over a year. But then the FF film released. And it tanked. It was the product of Sakaguchi, who called the shots on nearly every facet of concept development at Square, and Suzuki, the old-school business man who ran the money and left all the smaller crap to his second-in-command, a man named Yoichi Wada.
Suzuki and Sakaguchi were the brains behind Square of the 90's. Sakaguchi thought a change to Nomura's art style suited a new generation of consoles, Suzuki envisioned the necessity of the CD, they both created the concept of having two concurrent teams making FF games at the same time, etc. And they both envisioned a massive CG development studio in Hawaii that would revolutionize games and simultaneously be able to create films as well...
So naturally they both caught shit for that. Now while the Suzuki/Sakaguchi plan was for the huge dev studio to recoup costs over time, even they overestimated, to their fault. The board of Square began to panic at the notion of recouping the entirety of the costs immediately, and it was perpetuated by the constantly reported losses of the film. Upon the film failure, the board naturally told Suzuki to shape up, increased Wada's role, and essentially lost all faith in Sakaguchi. This was the beginning of the end of Square, and it's name was Yoichi.
Wada thus moved in and took on a much larger role, relegating Suzuki to having to go along with his vision of a massive developer/publisher that relies on its tentpole franchises. Development costs were streamlined (read: cut), projects were cancelled. Suzuki, and more so, Sakaguchi, hated this idea, and hated the development reforms Wada implemented to make it happen. But when Enix started getting gun shy about the merger, it was all Wada needed to convince the board that Suzuki's model was a disaster, and his was the future. Suzuki's last true contribution to Square was finalizing the Sony stock purchase, a testament to the relationship Suzuki built with Sony over the years.
Wada also hated Sakaguchi, and feared he would make a decision that would screw him over like he perceived the FF film did to Suzuki. So he essentially boxed him out, relegated his role in FFXII to almost nothing, and continued with his plan to cancel a bunch of non mainline franchise projects. It left Sakaguchi with no choice but to leave as he was essentially no longer a part of the company. So he did.
Square and Enix merged, and Wada's vision was now super strengthened with DQ on board. What else do we need?! The idiot. Suzuki was relegated further to 'special director' after the merger, then fully resigned two years later. SE was Wada's now, and the rest is history behind the workings of who I believe to be the most incompetent, unprepared and short-sighted company head this industry has ever seen.