That's a good point about the Academy having its own frat-like societies, and how dissolving the command track could have helped break their hold on Starfleet's culture. I wonder if Voyager was an early step in that direction, and the inspiration for that mechanic in STO: the show emphasized Janeway having been a science officer, and they described Voyager itself as a science ship (and, in the same time frame, the Defiant as a tactical ship), as opposed to the Enterprise as a ship-of-all-trades.
It's easy to imagine how, with that sort of specialization already emerging and with command cliques like Nova Squadron causing disastrous scandals, and with the Federation already moving toward a more versatile culture with the dual citizenship program and flexible uniform requirements (for more Zen shop costu... I mean, to reflect a greater tolerance for different cultures ), the decision to let any career track segue into a command role based on merit alone would become the norm.
If "Tapestry" is any indication, to be science track was looked at badly AND a career dead end. Seeing what happened to Picard in that alternate timeline makes it very clear to me that something major had to have changed on the way to 2409.