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Availability of New Content Without NPCs
In original BG2 there was almost never a need to bring a specific NPC along in your party to do a certain quest, meaning that the questlines and loot were available to all. Failing actually getting a quest, it was usually true that the player could wander into the area and kill things and collect loot regardless. In the cases of the NPC storyline quests, where you do actually need them, they were typically very short and provided no novel items. In the enhanced editions you have to bring the specific NPCs along to access new content, and therefore a lot of the new quests and loot are only available if you take those NPCs into your party.
As to how exactly to fix this... well that is a pickle now that the game is already at this stage. Adding dialogue options to allow you to go undertake the quests without them doesn't really make sense in a lot of the cases, considering how the quests are setup, but it might be do-able with clever writing. Another option is simply opening the areas up for wandering and wanton slaughter and looting sans quests, making most items available via shop or body. For example, in BG1, have the people Dorn wants dead always be there so anyone interested in elven chain can get it without needed Dorn, assuming they're up to murdering some seemingly random punks.
Of course I can always edit in items I want really bad, but it would be nice to be able to get the stuff without cheats.