Completely agree!  QBO is a nightmare for accountants.  

My issue is that for two new clients, I entered previous transactions manually through April 30, and reconciled those months.  I set up the bank to sync as of May 1, but QBO went back and messed with something and that forced a $16,949 reconciliation entry when I reconciled May.  I cannot figure out how to fix this, it should be as simple as reversing an entry that was made automatically, but you can't see where these phantom entries come from.  Similar thing happened on a credit card account for a new client.  

I'm a LONG time QB user, and in general have always appreciated all Desktop versions because they are true double entry systems.  QBO is truly "trying to do too much" as you mentioned.  Every accountant I know hates this version.