Who in the set is really worth collecting?
Surely that's a matter for the market to decide. There are plenty of examples of a card being valuable, even though the player on the card is no great shakes. Does anybody want any Billy Ripken card that's NOT a 1989 Fleer? When there's only 10 copies in existence of a card, it doesn't take much. Even if you could show that there were, say, 5 extra sets printed off, I don't see how that makes the cards worthless. And if they are worthless, they're my cards and I'm doomed to pay 1 cent rent on them for all eternity, or I can chuck them in a box and nobody will ever see them.
One of the characteristics of a free market is that things tend to wind up with the people who value them most. Maybe I'm the only person in the world who thinks these things have any value. If that's the case, then I'll be dead and buried before I ever sell them, but it's probably the same with 100,000 other items I own. By definition, every card in my port is something that nobody was willing and able to buy from me at my asking price.
Like you say, back in the day, even the commons from this set were $100, and the stars (at the time people like Travis Lee and Kerry Wood) would have been offered at shows in the $1,000 to $2,500 range. And while there might not have been a corresponding pile of cash for the cards, the cards would have easily traded for other cards in that range if the seller was willing to trade.
COMC auto accept is currently set at 35% off.