This is how I think they should do it:
You are captured by mind flayers and stuffed into a pod with very little room. Therefore, only the armor you were wearing when you were kidnapped should be what you have on you. You shouldn't have a pack or dagger or anything but the armor on your back. The mind flayers magically stripped you of everything but what you were wearing.
So, when you start the game, I don't think you should even have a weapon or a shield or anything. And there really isn't a point. They could make it so that in the first two chambers you search them and find a few weapons on the dead bodies. Boom. There's your starter equipment.
As for the weird custom armor they have on the origin characters, Shadowheart's looks like custom plate armor, or at least half plate. Whatever it is, I made it so that it was typical armor except that it didn't inhibit stealth. It's armor that is custom made for a cleric of Shar who is of the trickery domain. She should have something that doesn't hinder her stealth.
The same kind of thing for Astarion. Fine. He wears Padded Armor. So I made it custom Padded Armor that doesn't inhibit stealth. It also provides him with "hidden pockets" making it so that he gets a bonus on pickpocketing and such.
Wyll should be forced to be a Warlock of the Pact of the Blade. That's the only thing that makes sense in order for him to wield a rapier. Warlocks aren't typically proficient with rapiers, and the only way he could use one is if it was his Pact weapon. This makes the most sense for his character and it should be a forced build just for him. Either that, or he should not be proficient in rapiers.