There are other reasons to avoid GAE -- price, datastore latency, lack of flexibility -- but my main one is that GAE just doesn't apply to most of the things I use Flask for.
The other thing for me is that I have now spent time and invested hours into learning the App Engine platform but I get almost nothing in return since moving requires me to re-write or re-learn other tools anyway.
Unless I was a 100% committed to App Engine I don't want to launch a new project on top of it.
It took a while, but I really like Heroku's workflow so far and I feel like I have to jump through a lot less hoops. For me, it's the perfect middle ground between buying and admining some ubuntu VM somewhere and GAE's deploy and hope it works style.
I'm still bemused at how much of a free quota you get on GAE. I've had days with a few thousand hits, that doesn't even take any of my daily quotas above 35%.
Unless I'm wrong about GAE...