Meteor recently acquired FathomDB. Additionally SQL is on the cards too (http://roadmap.meteor.com) they're not exactly heavily invested in MongoDB. If anything it looks like they're giving users the choice of what to use.

SQL is on the to-do cards since "Nov 2, 2012" ... and lot of the comments are requesting it as critical feature

If you've used other db like OrientDB, you can use SQL to query documents. Even if MongoDB added this I wouldn't rely on it, as there have been many deployments that couldn't scale properly due to MongoDB and ended up switching to another vendor. It already has the reputation of being snake oil salesman of the DB world.

I'm curious what you meant by MongoDB being a barrier to entry?

My understanding was that, for better or worse, Meteor abstracts a lot of that from the developer.

Were you unhappy with the queries that Meteor generated?

Or did you find your application did not perform well, or in the way that you expected, and you believe this to be the result of the queries?

Or were there issues on the deployment/operations side of things?

Meteor in no way abstracts MongoDB away from the developer. Meteor is very tightly bound to Mongo, and Mongo permeates every aspect of coding in Meteor.