How exactly is the calendar an embarrassment? Maybe if you use a PC. My calendars are at all times synced between my iCal, google calendar, and my iPhone. The 3.0 update will make the calendar even better. The notes feature does what it says it does. Every notes app that came with my old palm pilots did absolutely nothing except save text. The additions to be added with 3.0 will, of course, make it even better. And you want a to-do app? Why don't you just pick one of the dozens on the app store that are free?
You can't set repeating alarms for anything a bit advanced. (ie, a meeting the 2nd Tuesday of each month). If you miss an alarm it is never repeated. It takes 7-9 clicks (plus text entry) to enter an appointment vs the 1 click (plus text entry) it takes on a Palm. If two alarms go off at once, only the text from the first is displayed. If you get part way through entering an appointment and then accidentally quit out it loses all your changes. You can't display a calendar of the year. You can't search your calendar. There is no snooze button for alarms. There is no independent volume for alarms verses game / music.
Notes doesn't allow you to sync. Doesn't allow search. Doesn't allow sorting. Doesn't allow you to categorize anything. Doesn't allow you to mark things as private or password protect a single note.
You can replace the to-do list with a 3rd party app, but you still don't get any syncing or reminder notifications.
The 3.0 update will address some of these. Notably the syncing and searching. Keep in mind that even the Palm or Clie you had 5 years ago could do all these things above. The Pre will be able to do even more.
The iPhone is a great phone. But sadly, not a great PDA.