Premising that the game is so messy it would probably faster to remake a new whole game(aka Soulframe what an original name...)
First of all i would remake the whole combat system because it's clunky, messy, slow and outdated but DE clearly has no idea what a roguelike(lite) is or what makes Dark soul so cool.
The damage system at the beginning was cool but at the end it revealed its uselessness with people practically using the same 1 or 2 elemental. This because when you make an OP game where the desperate enemies run away from you crying you want just kill everything careless of their weaks just spamming 1 button. Combined elemental actually has no benefits(WHO IS USING GAS ANYMORE?) excluding some niche boss fight(radiation).
At the beginning they released a frame because some missions required it but after a while they started to release frame increasingly more powerful(clearly because more power more sells) with the results we have today.
The Mastering system is probably some of the most time consuming exist in the game industry with the downside you practically don't learn anything, this why new players complain about the MR tests, probably the most fun thing in the whole game.
No endgame after 10 years means people like me will try your new quests, trying the new missions for a bunch of hours and closing the game again for at least 1 year.