Ah, I see. Changing which abilities can be selected as innates...
Obviously you can't add Command abilities. That leaves Equipment abilities and Stats up abilities.
Support ability checks are probably hard-coded in ASM (e.g in the Sword attack function, double damage if the "Dbl Grip" bit is set).
It would theoretically be possible to add, say HP+30% to the list, by tweaking in ASM. You would have to look up the routine for equipping abilities, and find the code checking if the HP+30% ability is equipped. There you would add a check for the bit you want HP+30% to use, and write (or point to) code that adds 30% to the character's HP.
The result of this would be adding HP+30% to the "list" of Innate Abilities. You should also disable the checks for the ability being overwritten.
Tedious, I know - but it seems all the easy stuff has been cracked. Some time, probably next year, I'll write some documents about ASM hacking.
For now, I recommend instructrtrepe's C2 disassembly doc found around the forum, and the disassemblies among the official docs.

ROM editor feedback updated. Some nasty bugs are found.