I know this isn't necessarily the best place, but it's a suggestions nonetheless.
In our old system (Authorize.net), if we processed a credit card in-house, the donor and relevant people in our org would still get a notification email.
With BBMS, they don't. Running them through BBNC isn't always an option.
BBMS also doesn't allow an easy way to print receipts from these transactions (we give these to our BO for audit purposes). If I open the transaction details and try to print, it cuts off most of the window.