There are only two things I've noticed myself missing:
The ability to turn the phone off and have it turn itself on at a predetermined time. I used this every night on my BB; I'd set the alarm and then shut the phone off to save the battery.
Customized sound profiles. I had one set for work, for example, where everything was silent except for phone calls and appointment reminders, which would vibrate. This was the setting I used when I was sitting at my desk. I haven't found an easy way to replicate this yet, without manually changing notification preferences for different types of messages each time.
The only other difficulty I've had is adjusting to the notification light; I'm so used to seeing that little red blinking light, but on the Incredible it's yellow and not as bright, but I'm sure I'll get used to it.
Lastly, I love the alarm clocks on this, especially being able to set multiple alarms as opposed to just one on the BB.
Overall I LOVE this phone, it's so much better than any BlackBerry I've used. Keyboard is excellent too.