That's the common pattern. MongoDB is easy and convenient when you first start using it, but you hit the limitations pretty quickly. I had the same experience.
All other aspects about it I love, though. It really makes development and deployment so much faster. Replica sets aren't perfect, but setting up MySQL replication w/ automatic failover on three or more machines is a recipe for disaster unless you have a DBA to sit there and baby sit it full-time.
[1] To see an example of the difference this makes see http://blog.pythonisito.com/2011/12/mongodbs-write-lock.html