I too have had this problem, but am too unsophisticated and my practice is too small to spend a lot of time on it, so I'm back to submitting by US Mail.
I just spoke to one of my major payors, however, and they said that they like having Office Ally submit the electronic claims, but I can do so directly, without them.
All my EMR system has to do is submit the data in ANSI-837 format. I could get an outside service to do this, but it seems like just a formatting issue. I would be willing to pay extra to have AC do this. The information is there. It would be OK with me if AC partnered with one of the vendors of this reformatting software to make this as seamless as possible.
It does seem silly to have an EMR system, print out the CMS1500, then mail it in an envelope when the payors are requesting electronic submission.
(Editorial comment--they're the ones with the capital. They could get their IT dept to make a fax reception number take every typed/computer generated 1500 as a pdf file, OCR it, and put these data into whatever format they wanted. It would not be difficult, given the uniformity of 1500 forms. AC could then just fax in the form it already produces.)