One killer for me is that GAE doesn't support running scripts outside of web requests. Webapps need cronjobs to do things like sync or cleanup data, populate news feeds, perform analytics etc.
Look at it this way, most batch jobs are prompted by a need to either import or export data; which is perfectly doable with GAE by having URLs for loading and reporting.
If you need to load gigabytes of data and run hours long procedures on it, GAE is the wrong tool.