MegaStore is the low-level storage system that Google uses. It is being replaced with a new system called Spanner (both being descendants of BigTable).
While Spanner was being developed, F1 was being created to act as the database system. This is meant to combine the scalability of BigTable with the usability of SQL databases.
To answer the question, F1 is different from MegaStore (now Spanner) in the way that a SQL database is different from the actual data storage system. I would imagine that Google will eventually offer F1 on the Google App Engine as Spanner replaces MegaStore.