1. Slightly randomize scripted event conditions, e.g. make vampire bat appear at 300 +- 100 JP or spawn Creator at slightly random places (although I believe fishlicka already does that in um... other boss fight).
2. Also do something with vampire bat script exploit which breaks it if you go into the basement (e.g. either continue it from the point you've left into basement or alter the course of events with vampire bat... which btw can still slowly suck on you through the roof of the abandoned house, but maybe that's intentional cause it's kinda cool)
3. Also if vampire bat character gets developed, maybe make some more random appearances of him on arbitrary JP values until you complete some scripted quest or task with him so he stops sucking you from time to time
4. Make some internal decision table or whatever which will alter the course of dialogs and NPC events for replayability (e.g. if I force Ingot to drop from school with me in the beginning he should already be there by the time I drop into fortress after title sequence and reply differently)
5. Also make some dictionary to randomize absurdistic answers and dialogues with NPCs after you've completed main hard-scripted ones
6. Generally randomize placement of key locations such as abandoned house, saloon etc
7. Allow to offend old man so instead of giving pineapple to you he attacks you with it or at least hides it from you
8. Add some global world characteristics which will alter after you fight bosses and return from boss area to the fortress so it gives you impression that you've teleported to a new world (although this needs to be carefully thought out since you can return from boss areas without portals)
9. Add some consequences to drinking your future self, e.g. if you drink it, you won't be able to continue the game from the checkpoint or you will lose all your stats and/or juice after death
10. Legendary monsters and maybe some unique locations randomly hidden in the plain. Although I am in doubt on this one since repeating nature of the plain gives you transcendental impression of the infinite and inexplicable nature of the universe precisely pointed out by Mrs. Slithers in her pop quiz: "is there anything out there in the fog"... which in turn gives me another idea that you can actually loop the world so if one continuously flight in one direction, he will sooner or later return to the fortress, which in turn can fix all the issues with large monster levels without ruining the game with invisible walls or other limiting measures
I am sure fishlicka already had most of this stuff in mind but anyway...