Not everything can be done through modding, even with WeiDU. A "hardcoded" limitation is something that can not be modified without rewriting the program itself.
You cannot make a mod that allows more then six people in a party. Monk/Sorcerer, Barbarian/Bard (etc) Multi and Dual classes. Item usability flags for custom kits. Animation slots number and their numerical IDs. (This one is not hardcoded in PS:T and can be easily modded). Number of entries in SONGLIST.2DA (100 physical rows). Hierarchy of random treasure 2DAs and their usability. Fixed musiclist.2da. Visual Range. Spellbook size. Number of displayed kits. ("Having more than 9 kits per class in the GUI" would perhaps more accurately be "having more than 9 kits per class per race in the GUI" (since it's perfectly possible to have f.ex 9 fighter kits for humans, and 9 completely different fighter kits for elves).) Turn undead/bardsong/thieving buttons. Having more than 24 HLAs in the GUI. Having more than 9 kits per class in the GUI. Changing the count of chapters. Foot circles are also hardcoded to specific animations. Original walking speed is also there. Changing the buttons to fit your needs, like a ranger using thief skills etc. The maximum size of TIS files is 60x80 tiles (though it is safer to use 59x79 as the max size) The maximum size of inventory BAMs is 64x64 (it gets all off place if it is bigger) The number of spell display icons in the GUI for a Sorcerer to learn The number of spells a Sorcerer can learn in his spell book The max number of attack per round is 10 The max number of stat is 25 The max number of reputation is 20