2 Things:
First, Sega's only real income is Sonic. Their other games don't sell that well, because they don't have that strong franchises. They also can't afford taking too long time to develop a very good Sonic game, but have to throw out like 1-2 a year.
Secondly, I do not think Square is doing a good job. The Final Fantasies are only popular because of their name. They certainly aren't really good games, at least so do I think. The last good Final Fantasy was VI, and only IX was close getting back to the series' roots, but not entirely. The others were, in my opinion, horrible games. Dragon Quest has stayed the same, as well, and not really developed. The other Square games are not really that well known, and all of them, are, in my opinion, either bad or just old concepts digested again. The World Ends With You was a pleasant surprise, but only that.
Square is one of the worst companies nowadays, actually... they don't produce quality anymore. Final Fantasy is just a cash cow, much like Sonic. All Square is doing is improving graphics to make the summon cutscenes be even more breathtaking and that's basically it. The scrapping of the round-based system only takes away more of the series' charme and makes it even more "0815 RPG"