It may not be philosophically compatible with GNUCash, but adding all of your accounts to Mint would bring it all into one site that you can then script against

It may not be philosophically compatible with GNUCash, but adding all of your accounts to Mint would bring it all into one site that you can then script against. Mint used to use Yodlee’s APIs to access data from financial institutions, do you could try getting developer access to that if you wanted something more direct.