You know, I had to really think about this. What are all the things that people have a problem with in regards to Square? Not enough innovation or too much? What made Square a great company in the past and what could make them a great company from this tragedy? I think I found a decent answer. This will be a long read so I'll warn you beforehand.
First, Square needs to let go of making Final Fantasy. I personally haven't played since X. The reasons are various. It was a milking of the franchise, there were better games, and XI was all about the MMO. Now, they have two MMOs and one was panned. The MMO model is based off of Blizzard's with nary a look into why Blizzard has so much success. XI was centered around team play exclusively. I'm not sure exactly why XIV was panned so terribly but it made Square an evil name in a few households.There's two too many MMOs with not enough resources from Square
Second, Square hasn't exactly fostered many positive opinions within the gaming community. Most people have sword off their remakes of their best games, leaving other game in the dust. We can name ALL of the Final Fantasy games remade, and yet the more eclectic games considered "niche" aren't available to all. Games such as Vagrant Story, Chrono Cross, or Tobal are not even given a chance in the new market. The consolidation of content has hurt Square, not helped them
Third, Square's forte is experimentation. People loved their old school games that seemed to push the limits. However, nowadays, it's as if they want to stick to telling a specific story. They aren't a movie service. When they tried that, it failed miserably. Square needs to go back to innovating. The World Ends with You was a successful experiment. So was the FIRST Final Fantasy. Xenogears, Chrono Cross, could have been greater if they allowed those experiments to be seen through. Experimentation > reiteration
Finally, Square needs to reconnect with their fans. Crimson Echoes and Resurrection would have been great projects, showing fans' support if they had picked up the team. Other projects could have been started and kept money flowing into Square's coffers. They chose not to, bringing out the lawyers. This is truly what has caused a bunch of fans to either go underground about their projects or just to move on to places where they can be appreciated. Since Valve has given so much, I'm sure Square can learn a lesson. Do not piss off your fans
Maybe I'm off base, but if Square had done a lot more to appease their fans, and less to appease stockholders, they wouldn't necessarily be in such a tight spot.