I wanted to follow up with an official “answer” on this one following our recent announcement.
There isn’t a consensus for whether Yodlee is better than Plaid or vice versa. Some institutions work well with one but not the other.
We do now have some official workflows to help clean up the duplicates if you decide to change the aggregator for a connection.
If a connection is working well we do not recommend that you change to the other aggregator. We encourage you to change only if a connection has persistent connection issues.
If you do decide to change, this is the best workflow using the new Data Cleanup tool for dealing with the duplicates. It’s still some effort, but it removes the need to identify and clean up duplicates manually.