Vault Dweller have you considered making every party member a nonstandard character in gameplay terms? That is, none of the NPCs could ever have been rolled by the player, in the same way you could not roll Nordom in PST. This obviously means you couldn't design 10+ companions, but I think it fixes a lot of the issues and makes things a lot more interesting.
Consider the typical issues where you have a primarily skill-based character system and parties without party creation. Nobody wants Jack the Rugged Sniper to be so good at sniping that the PC feels inadequate when rolling a sniper - but people also get frustrated by lugging around Jack the Blind Sniper with suboptimal stats. Furthermore, as you say so yourself in the update, symmetrical party members means it is far too easy to cover most/all skills. Even if we gate party members with CHA, it just becomes really tricky to balance; it'll be easy to have situations where CHA becomes a must-have stat and people run around with a party that can do anything.
But what if the kind of NPCs one recruited were unique mechanically? Not just at the level of Minsc has only 2 quick slots, but built in ways that the PC simply cannot be. Morte has his own unique skillset and equipment, such that he's never quite the same as a second fighter TNO. Obviously this is part of PST's JRPG influences, so that you can look at FF9's Quina, whose ability to learn and reproduce enemy skills is unique. Of course, the characters would have varying levels of mechanics overlap - so that maybe one guy has a unique weaponset but can learn many of the PC's non-combat skills, etc.
Obvious downsides are the effort involved and that the lore may forbid sufficiently interesting ways for the characters to be unique. But after the delight of AOD, I would hate to see the colony ship become like WL2 where it really doesn't matter wha5t the skill check is because every party has every single skill imaginable.