Largely the issue is that Matsuno left. Even though the original TA wasn't directed by him, he was still a part of the project as a producer and so forth. Hell the writer of FFTA itself seemed to be relegated to a more minor role by TA2's development.
Honestly its just a franchise that really was the vision of one guy and when he left the team just didn't really know what to do with it. Bolivar brings up Tactics Ogre but that right there proves the point that this team's skill really is about dancing to Matsuno's tune as I would be curious to feel if he would feel the remake would be the same without him.
FFTactics pretty much set a precedent about the series, and most of Matsuno's early works with Square (FFTactics, Vagrant Story, FFTactics Advance) at their heart deal with complex issues that tear at the heart of the players own world views. The man has a knack for writing moral quagmires filled with emotional landmines and then he expects you to walk through it as you play the games. I mean at its heart, Tactics strength is the tale of Ramza and Delita, the Lucavi and Lion War are simply backdrops to the twisted tale of these two men being forced though the flame of war and hardship and testing their ideals and resolves, its a character play about the reality of good men either being forgotten and cursed for their good deeds or becoming the very evil they seeked to get rid. The last sequence with Delita at the game's end perfectly brings home what FFTactics was really all about.
In Vagrant Story, once again its not so much the issue of political maneuvering and family secrets that is important to the story as much as it is Ashley struggling to find himself (in truth, I would argue Ashley's story is ultimately a better written and less idealistic version of Cloud's story from FFVII) , to watch Sydney rip from under him the very foundation of who he thought he was, and slowly facing the demons of his past. Despite fighting dragons, demons, and evil spirits the game and the cast make it a point to highlight that Ashley himself is the scariest monster of them all and so the story is an issue of mking the player ask the question if its possible for bad people to find redemption. Ashely himself never even gets a real sense of closure, simply choosing to hold onto an idea of who he wants to believe he really is but by game's end, neither Ashley or the player really get to meet the "real Ashley Riot".
FFTactics Advance has been gone over already but really I feel the kiddy nature of the game was perfect for telling a story that for most gamers hit a little too close to home. The idea of escapism into fantasy worlds to escape hardship. The tale just wouldn't have worked as well if the cast was older, it has so much more bite because Marche and the cast are kids and adults often see that time as a point where kids can indulge in selfish desires and escapism; so to watch it taken to an unhealthy extreme was really chilling.
FFXII has Ashe's story but part of me feels it lacks the real bite of the three games I mentioned. It may have been different had Matsuno saw the development through but that is largely baseless expectation at this point. Revenant Wings feels completely out of place because it wasn't made by the same team, just borrowing a few members but major players like Jun Akiyama were absent for that project and it shows because the game largely just steals ideas from the directors last project of FFX and X-2. TA2 is just a game without someone to focus it and it shows, the main plot is weak, and largely borrows ideas from the Never Ending Story, in a way I sometimes feel it was written this way as a means to compensate angry fans who thought the first TA game was going to be a simple FF style version of the Never-ending Story nd got slapped in the face by the stories heavy subtext. Even the few high points in the game just lack the gut-wrenching qualities of the early works. Its a fun world but it lacks the soul that Matsuno puts into his games and it shows. The man is a master of sleight of hand in his writing and design, always presenting you with something that seems simply only to discover too late the deeper subtext of his work.
Now if you'll excuse me, I need to rub some "brown" off my nose...