Charging by USB can take a long time because of a discrepancy between the iPad's power requirements and USB's energy output (which varies). This also explains why Apple included a 10-Watt power brick with each iPad.
Document management (and lack thereof)
iTunes document syncing is useless. I'm supposed to go to iTunes, click on the iPad icon, click on the Apps tab, and then scroll down to File Sharing? No. Not going to happen. I imagine future OS updates will fix some of these issues, but in the interim this presents a great opportunity for developers who can solve the iPad's document management and editing problems. (Google and Dropbox, I'm looking at you).
You can have the Bluetooth keyboard or the virtual keyboard, but not both
You can't use a Bluetooth-based keyboard and the virtual keyboard at the same time. Worse, you have to turn Bluetooth off to activate the soft keyboard even when you're outside the physical keyboard's range.
Where's the manual?
Joe Wikert poses an interesting question: Why is the iPad user manual not loaded on the iPad itself? While we ponder that one, you can read/download all 154 pages of the online manual here (PDF).
I'll post more as I run across them. Please weigh in with your own nitpicks through the comments.
- The first 5 things I noticed about the iPad (O'Reilly Answers)
- How to sync multiple Google calendars with the iPad (O'Reilly Answers)
- How to move all your Kindle books to your iPad (O'Reilly Answers)
- iPad-friendly browser-based programming environments? (O'Reilly Answers)