I have submitted multiple electronic plan reviews to several jurisdictions, and with jurisdictions that outsource to private plan review companies. Only one time was it faster than a paper submittal, and I suspect that's because the plan checker himself didn't really care to check closely. The biggest problems encountered are:
1. Poor user interface. For example, one major plan check consulting firm has a system where you can completely upload the plans, and it will tell you that you are successful - - but then you also have to press one more small/obscure button that says "submit", otherwise the software will not inform the plan checker that it is there to review. Yes, it was my problem that I missed the button, but I have since found out this is a very common mistake.
2. Sometimes a pdf gets corrupted or has something goofy happen to it. The same company in #1 above could not read some pdfs that were clearly readable in our own versions of Acrobat and Bluebeam. I had to send the plan checker hard copies just so he could proceed with the digital review.
3. Some plan checkers are more inclined to make a written comment on an 8.5x11 piece of paper, when it would be much more useful to point it out on the plan. (Bluebeam would be a tremendous help here.) I recently struggled with an exit path convergence question for a long time until the plan checker was kind enough to message me with a his cel phone photo of him pointing to the spot he was referring to, as it was displayed on his computer screen.
4. I am a firm believer in face-to-face backchecks to resolve sticky issues, not to pressure the plan checker, but just to make sure we are communicating well. The prevalence of electronic plan checks has reduced the likelihood of getting a face-to-face meeting.