Clock & alarms: you're right. A world clock is absolutely missing.
Contacts: right again. Should be way more customizable.
Messages: why isn't it even possible to save drafts?
Web browser: no text rescaling (believe that's coming though) and no password saving.

If support and FW updates for the N9 keep coming for at least 3 years, as they did for my previous (5800) phone, then we can expect some serious improvements (hopefully). About the N900, can't compare with that device since I never owned one. At the time when it came out, I didn't really have the funds but if I read all about what an awesome phone it was and still is, I'm starting to regret never having owned one