Since 2010, the Philadelphia Union has partnered with the Harrisburg City Islanders. The Islanders get Union players who aren't seeing first team minutes, the Union gets first look at players in Harrisburg (Sheanon Williams was signed from HCI midway through the 2010 season), and everyone wins.
Not everyone is happy with this arrangement though. The Union in particular seem to be exploring other options, sending out a survey yesterday to gauge season ticket holders' interest in a USL team. The Islanders for their part have tried to address their biggest need, petitioning the Commonwealth of Pennsylvania for a $5 million grant toward renovating their stadium. Yesterday evening, the Islanders sent out an email imploring people to email or send letters to the Office of the Budget to support HCI getting the grant. There are a few different scenarios that could happen, depending upon whether or not Harrisburg gets the grant.
If Harrisburg doesn't get the grant they could decide to renovate the stadium themselves, which is unlikely given the sheer amount of work needed to make the stadium anything resembling even a third division stadium (the current stadium doesn't have bathrooms, locker rooms, or running water). There are rumors the club would relocate to Nashville, which would make the transfer of players between parent and feeder club more difficult. The Union would most certainly balk at that. Harrisburg could conceivably fold if this stadium deal isn't done (although that's certainly a huge series of what-ifs and worst case scenarios coming true). Even if Harrisburg can pull it together and get a stadium, the Union may still decide to spurn the Islanders and field their own USL team.
With an affiliate club like Harrisburg, the Union don't get a say in how HCI operates. The Union doesn't pick the coaches or the players that the Islanders sign, and are only allowed to send a few players there at a time to play. Harrisburg owns the rights to their players (not the ones on loan from the Union). If the Union liked a HCI player, they'd have to negotiate with the club for the player's rights. There are no guarantees what benefits a player sees if sent out to the Island. That being said, this is a much less expensive option for the Union. Harrisburg foots the bill for the non-loan player's salaries as well as uniforms, equipment, field rentals, and all of the other expenses that add up.
If the Union had their own USL team, the entirety of the club would be run by the Union. All of the players's rights would be owned by the Union, and the Union would operate it according to their strategy. The Union could sign players - even if they weren't currently good enough to play for the first team - and work with them and develop them, eventually signing them to the big club. This seems like the missing link in the Union's long-term strategy of developing young players through the Academy and eventually allowing them to fight for first team minutes.
The Union have had to rely on Harrisburg first while they got the team up and running, and then while they worked on improving the infrastructure. They are far enough along that fielding their own USL team seems like then next logical step.