Proposal: when I already some games that is part of a bundle, I should be able to purchase the rest of the bundle at the same discount as the whole bundle, without re-purchasing games that I already own. I think GOG already does this.
Example: let's say games A, B, C, and D are part of a bundle. Each game individually costs $10, but the bundle is discounted 50%, so the entire bundle only costs $20. I already own games A and B because I purchased them individually. If I try to buy the bundle, it should cost me $10 because I am only receiving two of the games, C and D. (Note that I spent a total of $30 on the games in the bundle, which is still more than the cost of the bundle.)
Rationale: the current system is set up to "punish" customers who purchase games individually by making them ineligible for future discounts from bundles. I don't like this as a customer, but more importantly, I don't like this as a developer. Enticing new customers with a bundle sale is well and all, but I think existing customers should be eligible for the same discount. Customer loyalty should be rewarded, not punished.