When Suzuki and Sakaguchi were in charge, they wanted to create new IPs and not just milk Final Fantasy to death and they delivered on that promise. That variety and consistency of great titles we were getting is a big reason why people want a return to the Square Soft days.
Suzuki and Sakaguchi weren't allies; it was Suzuki who first capitalized on the CG movie mess to push the latter off the board (citing that Sakaguchi and ex-president Tomoyuki Takechi had forced everyone to go this route and that he had been powerless to stop it. As acceptance for that failure, he reduced his own salary). His vision for the future was the PlayOnline platform, which Wada more or less killed in favor of packaged offline software. Note that his opinion is that Square Enix should have abandoned HD game development, which is a huge burden for the company.
Furthermore, they all fell into the trap of milking Final Fantasy once the financial situation caught up. Remember the "year of Final Fantasy" that Suzuki touted, with the CG movie, anime series, three sequels, and a series of ports/remakes to be released in succession? Even Wada stressed varied IPs early on in his tenure, even if he thought in terms of mixed-media compilations instead of single releases.
Generally, Square management has been troublesome since at least the mid-90s, with everyone making a series of mistakes. As far as I can tell, it was only Alpha Dream's Tetsuo Mizuno (who led Square through the SFC generation and into the PlayStation era. That part about canceling Chrono Trigger 2 was a direct allusion to Sakaguchi's disagreements with Mizuno) who was committed to the vision of Square that we love. Even now, his company does the same thing, making little RPGs while rearing younger staff.