I upgraded from an S8 to the Pixel 3 and was also torn between the S9 and the Pixel 3. The $180 price difference made it an especially tough decision, on top of the Samsung trade in program that increased the S8 trade in price to $400...so the S9 would only have cost me $220 plus tax to upgrade to.
Ultimately I decided to get the Pixel 3 with the main benefit being stock android. Constantly disabling/hiding Samsung's duplicate app store, calendar, tasks, fitness, email, photo gallery and other apps gets annoying. I found a pretty effective method to disable un-disable-able (is that a word?) apps with the app BK Manager, but every now and then apps randomly reinstall themselves as Samsung packages certain apps with updates. There's even a Facebook app installed on the phone that I have disabled but it will re-enable itself when I do OS updates sometimes. This is pretty ridiculous for an unlocked phone. I can't imagine how bad an AT&T or Verizon phone is.
Additionally, after trying a Pixel 3 in store, I was really impressed by the screen and the usability of the new Android Pie gestures. The Pixel 3 screen is better than the screen in my old S8.
In my opinion, the only negatives of the Pixel 3 vs the S9 is the higher price of the Pixel, uncertainty around how scratch prone the laser etched frosted glass back will be, and the slightly larger bezels which isn't really a negative to many if you consider that you're getting better front facing speakers, and somewhere to hold on to while watching videos in landscape mode.