I agree with what you said at the start of your paper, "QB looks at money from the perspective of the business (the primary concern is where the money is coming from, going to, profit and loss, health of business, successful/failing programs). The people who gave the money are only incidentally important. Civi (or any CRM) is primarily dealing with people."
Because of this...We do not export our donor data to QuickBooks. We do not see the need to record who gave the money in both places. QB only holds the deposit information--when, how much and what campaign/fund the deposit is split into.
In Civi we have Financial Type to mark our Master categories:
Donations (Tax deductible),
Tuition (Not tax deductible),
Event Fees (Not Tax deductible),
This is useful for reports where you want to see all tuition payments for x time period
Line items are our fund accounts:
This allows us to drill down into more detail as needed
Customer = Fund accounting, this allows us to show income and expenses tied to our fund accounting. We can demonstrate to donors how much came in and how those funds were spent according to their designation.
Class = Functional Expense tracking, with each expense we apply it to Program, Management and Fundraising. At the end of the year when we do our 990, everything is already labeled. No need to estimate.
Department = Budget categories that different staff oversee.
This allows us to overcome QBs inability to truely handle fund accounting.
YES, as you pointed out we have to use a special report to split the deposits into the different funds/campaign before entering it into QB. We have developed a Drupal View that helps our Accounts Receivables more easily create the QB deposit entries from CiviCRM.
For my feedback: I am fine with your idea as an extension, it looks well thought out for your case use. I would make the argument that your paper starts off with the correct premise but then turns from that and treats QBs as a CRM--something it is not.
Thanks for taking the time to think through and write out your ideas on improving Civi!