What's better on webOS/Pre3:

1) Ability to patch the system to fit your needs. This is one pro among many cons of HTML apps, but it is a nice option. Possibilities are much more limited on Harmattan. I think that SailfishOS takes the best out of these two approaches (QML files are nicely patchable and the patch framework by SfietKonstantin is actually based on the webOS' one).

2) Hardware keyboard.

3) Gestures are nice (not saying better than those on Harmattan, but different) - app stacks and way you swipe off apps to close them are a joy to use.

4) Not sure if you've got a Touchpad, but the interoperability between the phone and the tablet is something the N9 truly misses. It doesn't live to its full potential, but sharing links or photos between devices with a simple touch is nice and very user friendly.

5) Account integration. Syncing Google Contacts/Calendar is a PITA on Harmattan, compared to webOS - their Synergy was quite ahead of any OS.

6) Wireless charging.

What's better on Harmattan/N9:

1) The community an the future-proofness of the device. While in my eyes the N9 is not as future-proof in this way as the N900, it still goes way beyond webOS. This is partly caused by some parts of webOS being closed - for example the Synergy is closed source and while the community tries to patch it every now and then, it will slowly die.
You don't see much development around Harmattan today, but webOS app development has been (unfortunately) conpletely dead for some time.

2) Packaging system - APT is not ideal (worse than Pacman or Zypper IMO), but is way better than IPK. It's hard to find useful packages in the extra repositories on webOS and most of it is very outdated. You can fixed some of it by chrooting Ubuntu, but there are problems with it as well.

3) Reliability. Now this is not for sure - my experience with the N9 was not long and I did not find any issues, but today, in hands of another user, it seems like the most unreliable phone I have seen (losing SMS messages, freezing, restarting, apps crashing, even after few factory resets).
Judging solely from my experience, webOS was less reliable - besides some crashes, it was mostly caused by one missing function - unlike Harmattan, webOS cannot wake up the phone when alarm is supposed to ring. I know that pretty much all modern phones (except Jolla) miss this feature as well, but it was a major drawback for me.

4) Higher quality apps - this is probably caused by webOS' unfortunate choice of HTML based development.

5) System logic - you can find many small features in the N9 that ease user's life, like Nokia used to do in its golden days. webOS seems more ordinary in this regard.


These are just my opinions - I think both devices are quite nice and neither of them is perfect