Wow, this has been a problem for more than 3 years.

Does Intuit have any plans to resolve this?

Adding "Wire" or "EFT" to the check number field is not a solution.

I usually use online bill pay through my bank and have always been adding the transaction number to the memo field, but that is a cheesy workaround, since it requires me to use "pay bills", then go back and open each in the check register to add the memo.

This also makes searching for a reference number a bit more tedious.