Well, better placement of cutscenes is a good starting point.
Whats wrong with the cutscene placement? FFXIII is one of the few jrpgs where cutscenes haven't bothered me. They aren't incredibly frequent and only last a few mins. Nothing like Xenosaga here.
Enabling better control over your party is another one.
Hardly needed if you ask me. FFXIII ai is fine. I know people have cited problems, but for the most part I can't think of an instance where I died because of the ai. Casting things happens so fast in the game so the order in which the ai does it doesn't really matter. Sab ai does suck though. Much better then something in Persona anyway. Plus the battle system is too fast for you to control each party member. Would an option to switch between them be nice? Yes.
Letting the player do more than make very general battle tactic decisions also goes a long way in to making the game more engaging.
FFXIII at least for me is one of the few non srpgs were I had to use something more then attack for most of the game. In pretty much every FF it just becomes the same tactics over and over. And while it's pretty much the same with FFXIII, I found most of the battles to require more thought then any other FF and mostly any jrpg outside of Nocturne. I guess you could point to auto battle, but I hardly use it and have no idea how anyone could complete the game using it is my choices are mostly better then it. Then again, this is just my opinion.
It also wouldn't hurt to see less reliance on a single battle mechanic that is little more than a combo meter.
I can't think of a lot of jrpgs that have tons of variety in their battle systems. Surly not DQVIII at least.
And then there are always the options of including actual world design to help with player immersion,
I had no problem with immersion. Sure lack of towns hurt this, but I hate towns. I got how the world was through dialogue and that's fine with me.
I'm not sure how the two worlds are not coherent. Things seem to go along fine.
I think FFXIII has one of the better FF cast and at least all of them play a part in the plot and are developed. They are anime steroytpes, but this genre is filled with them. I'm not sure whats with the hate of the cast when Tales games exist.
battles that can break you out of a trance-like rotation cycle that works in most encounter
Most of the battles require different strategies. And if this is a complaint against XIII, then I guess it's a complaint with most jrpgs. Almost every random battle in a Tales game can beat the same way. Same thing with DQ.
and a non-linear character upgrade system that actually allows for player variety.
The characters are all different thanks to how there classes are setup. Sure this achieved through pretty shitty ways, but characters are different then each other. And it's better then FFX and FFXII in that regard.