I think, for me at least, what they're missing is a diverse catalog and a sense of being progressive.

In the SNES and PlayStation days, Square experimented all the time and consistently brought out new IPs while keeping multiple series' going, all with cutting edge production values and design. The PlayStation alone had installments in the FF, SaGa, and Mana series while creating tons of new IPs like Brave Fencer, Xenogears, Parasite Eve, Ergheiz, and Vagrant Story. There was a real sense in the 1990s that Square was a very progressive company always on the cutting edge and starting new trends in the industry.

Now, they couldn't be farther from it. It seems like every game they put any amount of effort into always has "Final Fantasy" or "Dragon Quest" in the title, and games that would make for perfect new IPs are always released as spin-offs of one of those popular series. What few new IPs they do bring out always seem delegated to the mobile platforms, which I dislike, instead of consistently bringing out cutting edge and varied console titles with spectacular production values. I miss the Square that brought grand console role-playing experiences consistently and on a frequent basis, I don't want to see IPs with great potential having that potential squandered by releasing on platforms like iOS and Android.

So, I guess to sum it up, Square is missing a varied release schedule on consoles with multiple strong IPs, along with a willingness to experiment with new series.