The US Open Cup has made a rule change for 2016 which should lead to a smaller field next year. The competition this year featured MLS-owned USL sides, something which the competition won't be allowing in the future:
"Any Outdoor Professional League Team that is majority owned by a higher-level Outdoor Professional League Team shall be ineligible to participate in the Open Cup. The Open Cup Committee shall review and determine team eligibility annually pursuant to this provision and report its decisions to the National Board of Directors."
This amendment makes a ton of sense, as frankly, having B teams in the competition is both silly, and offers a potential conflict of interest. Cosmos B, however, appear to be eligible to compete, though I'm not sure exactly how.
Regardless, I'm glad to see the Cosmos won't have their B side competing, as I found it fairly annoying that USL sides such as Red Bulls II were in the 2015 field. Thankfully, they won't be next season.