Just curious as a Heroku user who wants to keep tabs on GAE.
Recently I've been doing a fair bit of traffic and I'm still below the $2.10/week minimum. If I get even more traffic I don't have to touch anything to deal with it. Heroku doesn't auto-scale quite the way that GAE does, it isn't transparent. Yes, I know there are tools to help with this, but GAE does it automatically.
A key point for me is that Heroku doesn't have the GAE Datastore. This might be fine for you, but the hope for my company is to get as large as possible and the last thing I want to think about is replication, backups and scaling of databases. I've done that before and it sucks.
People seem to quickly forget about the recent outages on Heroku. That said the past year on GAE has been pretty darn stable. I think they've really fixed a lot of the issues they were having early on.
I do use Heroku for two apps running in the free tier and I can't complain because they are free and they wouldn't be possible in GAE. I have a NodeJS webpage scraper (which is controlled from RESTful hits from GAE) and a reverse nginx proxy so that I can serve up mapquest OSM tiles over https. =)
So, maybe it boils down to the needs of your application and your tech stack comfort level (there is no Ruby or PHP on GAE).
On a side note, I love your business! =)
A bit of sub optimal design expense is nothing compared with hiring employees and it is relatively easy to refactor code to fix parts of your app that are costing money. I'm sorry the OP has to actually spend a bit of time thinking about how much implementing this new feature is going to cost, but that sounds like basic sound engineering principles to me.
In the end, I'd rather focus on adding features to my webapp than getting paged in the middle of the night when AWS/Heroku goes down or my site suddenly gets a lot of requests. From that aspect, GAE has been a lifesaver for us. =)