It would be nice to have suggestion 661286 Auto deposit of Cash Receipts in Bank as an optional feature that could be turned on for certain types of transactions, customers or accounts.
The current feature set makes sense when checks are being a physically deposited but in electronic payment scenarios where there is a real 1 to 1 ratio of receipt to deposit, having to create a deposit for each of the items is cumberson.
If you think this is a good idea, follow the link to vote for it.
