That would be a really useful tool, Rukiri! I think the number one request if you include squad combat is the ability to set up each member's AI similar to FF12's party formations and Gambit system, with a weighted list of "if-then" or "always" preferred behaviors that can be slotted in as desired, and formations like one of those springy web charts I can't rmember the official name of to set the party up in a rank or column, paired column, two ranks, wedge, or circle around a central character, with the main character's position in that formation also settable. Being able to determine range and whether a character has line-of-sight to use a ranged attack/weapon, and how far from the main character to pursue enemies before returning to formation would also be good, since I'd like to see more sci-fi games and even the generic standard fantasy stuff usually has spells or at least bows.
Perhaps make all attacks an arc with definable origin point, angle, and range? That would allow for any swung or launched weapon, though it would need to be able to nest a second attack origin/angle/range to handle spells or missiles that have a blast radius when they hit. Probably a targets-in-area and IFF counter too, to handle spells that can be cast at any single or finite group of targets within blast radius x smaller than range y. Theoretically infinite nesting would be a funny idea, but probably eat too much resources beyond something like a bomb that you throw and then bursts into several smaller bomblets. Oh, and one more effect, something to allow for "chain lightning" that hits an enemy and then shoots again to the nearest enemy hit the least number of times, for a finite number of hops within a certain maximum range from the most recent hit.
More generally, it would be handy to have support for a level system built in with an arbitrarily large cap, that can handle either directly modifying character stats in a predetermined way like classic RPGs or providing arbitrary points in an arbitrary number of pools to spend on improvements, the details of which would of course depend on the specific end use.
If you're doing user interface type stuff as well (which it sounds like you are) an inventory and equipable weapons/accessories/skills systems would also be a nice addition.
I mentioned a level system before, but character stats are also a near-constant aspect of the genre even without one, even if they're just HP per character and base damage per weapon. I strongly suggest setting it up so the number and types of stats can be arbitrarily large, along with exactly which one is used to resist which and how they are modified (skills/equipment/etc. as well as situational things like high ground or special rules for a boss map etc.) Being able to use a formula to calculate the effective value from the character sheet numbers (I like 2(x/5) myself as in the Champions tabletop RPG, though a system that scales so higher numbers are worth less absolute improvement instead matches better with real life) would also be useful to some concepts such as the superheroes genre that has gained popularity in the past few years with the Marvel and DC movies. Just being able to make the numbers very large, like the Disgaea games, can stand in well enough if that turns out to be harder than it looks.
Though not so much a feature of the games you mentioned (the only one I know for sure that used it was Brotherhood of the Blade on PSP) being able to set gamepad skill buttons on the fly by using a d-pad ring menu and hitting the button you want to set was also really useful, though that depends on what you intend to use for control inputs to begin with; BotB had directional control via left stick, one fixed right button for a standard attack, and the other three right buttons configurable that way. Original Kingdom Hearts was similar IIRC but had to be set up from the pause menu, possibly out of combat.
One last thing before I stop rattling on, support for fast travel in/on a visible vehicle or mount on the overworld if there is one, and especially if there ISN'T one - with a user selectable arbitrary number of vehicles. If it's just an open world rather than an overworld, the ability to put each active party member in their own vehicle or assign them fighting stations from a large transport for dealing with encountered (random or visible? Ideally, support both, with the system choosing from a set of text files for each encounter type in a folder for each zone, or at least an easily edited master list) enemies would also be good.