All of the points are fitting the description of long time partners like Square. They pour so much cash in them, might as well acquire them. FF is synonymous with a PlayStation IP. It would be better to own the rights then only to pay for limited exclusivity. Also speaking of teams being capable in creating new and fresh IPs. Square Enix has a drove for talent. Square has sheer potential when it comes to creative minds. In case of acquisition Sony would expand all existing creative business units and even create new ones. We should keep in mind that Sony had high ambitions for the anime market. The franchises of Square Enix are prefect suited for this ambitions. Plus they would get their first Manga publishing label with Gangan Comics. Another reason is also to protect the partner. Let's forget about Microsoft, there also other potential threats like Tencent. In my opinion it's the best time in acquiring a big company like Square. Sony should utilize this opportunity.
Square may not want to sell. And if they don't want, Sony won't buy them.
On top of this, Square has different non gaming/movie/music business areas where Sony may not be interested to own (books, magazines, manga, arcade games and arcade facilities).
Sony may also think that PS is the RPG machine and has that genre more than covered, so don't need to address them via 1st party, and that instead their 1st party has to grow instead in other areas like PC or mobile where SE does it ok but isn't a key player. Sony also may think it makes more sense for them to just paid timed console exclusives than to spend several billions to acquire them. Or maybe both were interested on an acquisition but Sony didn't have anough budget available and had to wait several years more until they get enough money. Or may consider that the costs of recent acquisitions are too high and are affecting too much to the profitability and may want to wait some time before making more.
Square said they'll turn some gamedev studios into subsidiary companies to allow external investors to own part of them. So maybe Sony will do this, buy totally or partially some of their studios instead of the whole SE.
Regarding new IP, Bungie, Firewalk and Haven has people who leaded the creation of new IP that broke the records of fastest selling new IP ever in gaming history. SE don't, and their main IPs are from almost 40 years ago.
On top of that, they may consider that regulators may block the acquisition.
I think it would be a good acquisition, and I'd like to see Sony expanding to arcades, mangas or books. But I understand that Sony has many reasons to don't want to buy them, or at least right now. Or not being able to do it now/soon. And also SE having reasons to not wanting to be sold.