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Hire people to work on the project, so their incentives can align with yours. Like, its worth more to you for someone to spend a lot of time on the important issues and less or no time on the unimportant issues, but pay-by-issue would lead to people avoiding the difficult issues (important or not). You can increase the bounty for some issues but I doubt it will work.

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I was just thinking, maybe you could accept (detailed) proposals, and then the proposal writers would make a small commission when their proposal is selected, and then the implementer would also get paid for actually doing the work. This would help filter out drive-by contributions and payment would be determined by the helpfulness and difficulty of the proposal and effort to implement. You could have a maximum number of payouts per cycle, as well, and be upfront that payout is only guaranteed after the proposal is accepted by whatever process you put in place for review. Be upfront with high standards for the proposal review process as well. Still, I think it probably won't work.

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