Some setup info:
Mongo DB primary: 2.6.3
Mongo DB secondary: 3.0.5
Secondary uses wiredTiger

When running an initial resync for an instance that contains 1000+ DBs, each with ~100 collections, with over 1000 indexes overall (per-db), the resync process is very slow. Specifically, the index creation process is very slow.
It seems that the index creation is performed one-by-one, without any parallelization between the collections or between DBs.

It would be wise to rebuild many indexes in parallel, to fully utilize the available resources and shorten the resync process.