The core idea is that CBS’ and Paramount’s differing viewpoints on the franchise might have frustrated Abrams to a point where, when Star Wars became available, he decided to shift his allegiance and master plan over to the dark side at Disney.
Basically it comes down to this: since CBS owns the rights to the all the Star Trek TV shows, it owns the rights to the characters. In order to make a Star Trek movie, Paramount must license the characters from CBS. (CBS and Paramount were once both owned by Viacom, but CBS broke off in 2006.) At the same time, CBS can do whatever it wants with the characters, independent of the films. This is thought by some to cause confusion in the marketplace. (Spock bobbleheads with “Star Trek” on them that have nothing to do with the movie, etc.)
On the 2009 Star Trek film, the two corporations feuded big time, creating a lack of licensing and merchandising. They worked together better for Star Trek Into Darkness, but the multimedia, multiplatform saturation of Star Trek is nowhere near as big as Abrams and his Bad Robot team had envisioned.
The bottom line is that, as far as I’m concerned, it’s a dirty rotten shame the way Star Trek rights got split up and it does indeed sound frustrating. It’s hard to properly market, promote, and saturate the market when the rights holders are feuding. I imagine being J.J. caught up in this ridiculous feud can’t be fun. It’s frustrating too because most of us Trekkies are over here saying to both companies, “Yoo-hoo, over here, take our money, NO REALLY, JUST TAKE IT!” Both companies could profit together, but noooooo, we can’t have that. And it just frustrates EVERYONE involved.
And of course at the same time, J.J. already loved Star Wars more, so “switching allegiances” as Germain says in his piece was probably a no brainer.