I've been in practice now for just over a year and am still submitting my claims only on paper. I started on paper bec. I wasn't a provider for any insurance companies so the e-billing service wouldn't give me an account. (I have a complicated setup where for legal reasons I officially work for 2 other doctors who own the office, although I run this branch and we run it like partners. Therefore, I was able to bill in their names as supervising doctors).
My secretary who does my billing has done so for 3 different offices where she has worked in the past. She says she has never been paid as quickly or as well as I have been and the only difference she can see is the paper billing. We are therefore going to continue with paper billing. I am actually being paid within 3-4 weeks for most claims.
One thing I'd like to add is that you should pay attention to the reasons that your claims are rejected, correct the problem and bill again. If there is no good reason, just bill again. There are certain codes that I never get paid for the first time around (like 99000--specimen handling) which I will usually get paid for if I rebill.