There could be a way to create custom companions and still allow them to have personality.
Take MotB. Safiya is a Red Wizard, there's not much to change. But Gann's character is simply "a free spirit and a dreamwalker", neither of which require a particular class. So, when he joins your party, a character creation screen could come up where you have to design his character from scratch, having to choose, however, among a certain pool of classes. For Gann, that could be "Spirit Shaman, Rogue, Bard, Warlock, Sorcerer", plus the available Prestige Classes. For Kaelyn, "Cleric, Favoured Soul, Paladin", for Okku "Fighter and Barbarian", etc.
This would allow for a customized party without sacrificing party interaction.