My list of important stuff:
Blade Grasp only vs blades
Text error correction
JP Scroll Glitch fix
Best Fit Glitch fix
25% PD undead
Weapon Guard innate all
Broken equip buyback (if possible)
Better br & fa for starting generics
Consolidated move-find (always get 1 item)
Enemy equips set or random (no "nothings")
Swordskill changes (MP/evadable)
Drain/%-based attack change (less damage to lucavi)
Charge skillset PA*WP+Y and MA*WP+Y (same sort of thing)?
More enemy unit variety (fewer battles made up of Wizards, Knights and Archers)
No perm br and fa changes
Special characters can do propositions
Mighty Sword hits monsters?
Death sentence ignores cancel: dead
Soldier office rename any unit
Formulas that use (MA+X)% become (MA*2+X)%? (MA is more important for status effect success)
Secret hunt not required for fur shop
party level cloud
Regen/Poison change (capped)
Party level story enemies
Gear scaled to story (Glain's ASM) (These last 2 are for added difficulty)
Remove Degenerators - FFMaster
Malak Formula Fix - FFMaster
Engineer learns equip gun
Swordskillers learn equip sword
AI cant learn skills that it can't use
Perhaps allow for Elemental to be evaded
Perhaps make Summon Magic do slightly less damage, but let it keep smart-targeting and instead boost other Faith-based magic.
Either completely kill Golem or let it add Protect.
If Knight gets ranged breaks, then it should be the stat breaks ala 1.3.
Knight's equipment breaks should become more likely hit, but should NOT become unable to be dodged.
Thief's equipment steals should become unavoidable.
Lessen the amount spells that Math Skill has access to.
Kill the CT Parameter.
Give Calculators better stats or, at least, close-to-average speed.
Make Speed Break/Speed Ruin add Slow or -20 CT if possible.
Make Speed Save add +CT rather than +Speed.
Kill all other speed-stat increasing or decreasing abilities like Cheer Song, Slow Dance and Ramza's Scream.
Kill Hamedo (turn Hamedo into firststrike?).
Separate MP switch and Move mp by gender
Cap WP for all weapons at 20.
Give Cloths less W-EV.
Give Aegis Shield less M-EV so it doesn't single-handedly shut down Magic with Abandon.
Strengthen weak weapon (types) that aren't Bags, specially (Long)Bows, Staves and maybe Rods.
Weaken all gender-exclusive equipment.
Make Knightswords and Katana's damage formula PA*WP.
Change or kill Level Blast and Please Eat. (Heh. Completely forgot about Please Eat.)
Fix AI flags on some skills
As for PA/MA/SP - Xifanie has a hack that buffs Maintenance to block breaks on these and puts an upper/lower cap on how much they can be boosted or broken. For something meant to embrace vanilla's faults while making them less outright dumb, this seems perfect here - you can keep Accumulate, Yell, Speed Break, etc. in all their vanilla deliciousness while removing the cheesier strategies most of them created in one masterful stroke.
More dubious stuff:
100% knockback throw stone
Ranged knight breaks OR unevadable
Lower range Lancer jumps
Limited calc skillset