Chivas USA was the only MLS team that had no presence in the first year of the MLS-USL PRO partnership, in 2013, and remained the only active team to not have a USL PRO affiliate last season.
We may have some insight now as to why that was the case.
In an interesting interview with Orange County Blues play-by-play announcer Marc Serber on the USLRadio podcast that was released on Thursday, came the fascinating tidbit from Serber that Chivas USA wanted an affiliate agreement with the Blues, which the latter club rebuffed (that point comes at right around the 12:00 mark). Serber doesn't specify which year this was (or if it was both years), or any further details about it, but that's pretty striking, considering both teams had some real turmoil the last couple years and still CUSA was evidently denied in the seemingly-logical quest to make the Blues their USL PRO affiliate.
Of course, in the long run, it's a moot point, since Chivas USA no longer exist and no one can deny there was remarkable turmoil and disfunction with the defunct MLS side. And the Blues are in the midst of a rebuild that seems to be paying dividends so far this year, while remaining a totally independent USL team.
Besides the brief mention from Serber about the CUSA-Blues stuff, I'd urge you to listen to the rest of the interview, as he talks at length about the Blues and how they've been doing this season. You can find the interview on USLRadio's website as well as the show's iTunes feed.
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