Honestly, there’s a lot of issues shiny hunting has made, and this is one of them. Originally, ID Pokémon were supposed to give incentive for players to join each other to get Pokémon that they normally couldn’t get. However, with the wave of shiny hunters, ID Pokémon become more of a hassle than naught. I would agree with you that removing them would be nice, but then an original function of PMU would be removed. (Not that I would mind considering PMD:DX has all the PMD Red and Blue Pokémon, so fully removing ID Pokémon would be nice.)
Percentages would be a nice alteration and would definitely be doable. It gives opportunity for people who cannot party up with people, but people would still prefer joining up with others to have that higher percentage. It’s better than nothing, but I feel like there’s a better way to make ID Pokémon more accessible.
I feel like having a consumable item to make ID Pokémon appear in a dungeon would be neat to have. Use the item and, the next time you enter into a dungeon, you would be able to see Pokémon you didn’t see before. It would be an interesting item that could also be an alternative. Plus it would be like a new Honey item on the market! I think it could be called “Vivid Scent”, in reference to Pokémon XD: Gale of Darkness! Which I made a thread for after posting this.