An app I’m developing has serious need for many-to-many database lookups-- way beyond what would make sense via MongoDB denormalization. Apollo will solve all this when it gets here (and in my case when Mantra integration for Apollo is available.)
In the meantime, what is the availability of MongoDB 3.2 $lookups in Meteor at this time? Is it ready to rock and roll? 
I’m afraid it’s still in development, you can check current status here https://github.com/meteor/meteor/issues/6957
If you dig into the various discussions on this subject, I think you’ll find that unless you need oplog tailing, you can get 3.2 to work today. See honmeteo’s response at Can Meteor 1.3.x be used with MongoDB 3.2? for example.
So, if your development is going to take a few months, you might consider developing with 3.2 now and risk either not needing anything that is broke or mdg fixing the issues in time. I’m fixing to bite into 3.2 (and the node 4 branch) myself, but I’m unlikely to be thinking of even alpha deployment before October or so.
I wonder… if you don’t need reactivity can you do a collection.rawDatabase()… call?