I agree with dillanger's point on having to reuse my AMCAS essays. That being said, I liked having to write the 3 AMCAS essays, and I think this will continue to streamline the process as the schools' secondaries catch up to the new AMCAS.
A lot of schools request/require 3 research letters. Not everyone has had 3 PIs. I had to request exemptions or substitutions from a few schools. None of them gave me a hard time, but it was still a hassle.
Some schools send you a complete e-mail from the med school, and then tell you to check by e-mail or telephone with the MD/PhD office. Unfortunately, some of those offices never return your message. Or they have a status page that only reflects your MD status. I guess this is because the MD/PhD program office is separate from MD admissions, but it make it difficult to really know your status.
If a school is not going to give post-interview decisions until January, they should not tell you to expect to hear in November or December. Correct information could've eased a lot of my anxiety while waiting for decisions (well, I'm still waiting, but now I know how much longer I'll have to wait).
Some schools list your interview status on the status page, but never send you an e-mail or letter about it. What if you don't check your status page? What if you don't realize that school has a status page? Would you just miss your chance to interview?!
The best secondaries can be submitted online, have atleast 1 essay (how does mailing you a check let you "get to know" me better?) but not more than 3, and only make you mail LORs to one address.
Schools that expect you to give their specific form to your LOR writers are obnoxious. My LORs were sent to the pre-med advisor months ago; it's a complete pain to go back and ask them to fill out a separate form, and then make sure the form and the letter end up in the right office. One school even requested that I get my LORs with a special form sent to me in sealed envelopes, and then send the envelopes with my application. And the form had to be signed by me first b/c there was a waiver. So, I had to sign and mail these forms to my LOR writers with stamped envelopes, wait for them to mail them back to me with their signatures over the seals, and then send them and my paper app to the MD/PhD office, only to have them LOSE ALL OF IT. Of course, my MD app (along with my check) arrived just fine. Needless to say, I got sick of the hassle and withdrew my app. Do they have to make it such an uphill battle?