According to changes to USSF policy, USL teams owned by MLS organizations will not be allowed to compete in the 2016 Lamar Hunt US Open Cup. The unannounced policy change appeared in a document posted on USSF's bylaws page this past September. The amendment in question reads as such:
"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."
There was no reasoning given behind the change, though it has been speculated that there were concerns about senior teams not wanting to cup tie some of their loaned players to their lower division team, leaving those USL teams undermanned and fielding untested academy players as a result. Seattle Sounders 2 was not a major offender of this with the exception of Aaron Kovar not suiting up for S2, but other teams, like New York Red Bulls 2 had seven players from their U-18 and U-16 squads on their gameday roster.
This likely means that there will be more MLS vs. MLS draws in the fourth round this coming year, as opposed to 2015 when the Sounders and Portland Timbers were the only matchup of that sort. Whether this is good for the tournament or not is something yet to be determined.