FFXI - this was a MMO in the style of Everquest. It made the company a lot of money.
After Spirits Within flopped, the series creator, Sakaguchi, left Square. He was the creative force behind the first 9 games. I think recent installments have felt lackluster because of his lack of involvement, but that's just me speculating on something fairly subjective.
FFXII - had a number of development issues, and the director of the game (Matsuno) left the project before the game was complete, citing health issues. You can start to see S-E falter here, second-guessing Matsuno and making him shoehorn in characters based on appealing to a larger demographic. FFXII was still a success, critically and comercially, but it was developed longer than it was supposed to, so went over budget.
Now, every FF is somewhat polarizing, because the series tries new things with every entry, but FFXIII even moreso. Lightning was designed to be a female Cloud, they took out towns and other things that made FF feel like FF. In the end, after being super hyped, the game was just ok. Many people complained that the series was going downhill. The same time FFXIII was announced, S-E also announced vs XIII, which was designed by Tetsuya Nomura, and was supposed to feature real time combat, and a more mature stab at the franchise. This game looked like it would be the answer for people who did not like the direction FFXIII was taking. FFXIII was released a couple years later, but information about vs XIII became more and more scarce. The ballooning cost of HD development hit a lot of Japanese devs hard, and so FFXIII-2 was created to help offset some of that cost by reusing assets from FFXIII while Nomura's team continued to work on vs XIII.
Meanwhile, S-E was working on FFXIV, another MMO. Basically, S-E had a cash cow with FFXI and they thought they could get away with releasing an unfinished MMO and add to it as they went on. A number of design decisions obstensively added to thwart gold sellers proved unpopular with the playerbase. The game itself was laggy and lacking in content. The market cried foul, and S-E realized they were hemmoraging good will, so Tanaka was fired, and they brought Naoki Yoshida on board to fix it. At this time, S-E took people off of vs XIII to help fix XIV. Once FFXIV was fixed, development resumed on vs XIII, which was now rumored to be renamed as XV. Meanwhile, people continued to clamor for a new Kingdom Hearts, but its development was on the back burner until Nomura finished XV. A couple years ago, S-E moved Nomura on to KH3 and had Tabata (director of Type 0) become lead director to help push the project out the door. We may never know all the ins and outs, but I bet Nomura butted heads with the powers that be (Wada?) over the direction of XV, leading to his being reassigned. I want FFXV to be good, but if I'm being honest, it will probably have the same designed by committee problems of its predecessors. Maybe it will be the dark FF with KH combat we've all been waiting for, but looking at how they've changed focus, I'm not so sure.
TL;DR - S-E can't make a good FF without the Gooch.