Connected Franchise is prominently featured in Madden NFL 15, NBA 2K15 still has online leagues (albeit their new MyLeague feature is not online-enabled), and MLB 15 The Show still has an online franchise mode. The only two we've lost over the past year or so are NCAA Football (we lost the game completely) and NHL 15 (next-gen leap). To say these modes have "all but disappeared" isn't really fair, IMO.
Here's the thing - a console sports video game has to attract people to play it beyond what the monetized quick-play modes offer. The game needs replay value beyond the pick-up-and-play aspect, and certainly needs to offer this without forcing the player into micro transactions lest consumers revolt. Sports games have offered season modes since their inception, and franchise modes since the turn of the century. Having a franchise mode is now an expectation of licensed console sports games, and a sizable portion of the audience now expects it to be there. It's an institutional component of the infinite replay value concept that sports games have, which sets them apart from traditional narrative experiences in video games; franchise modes are capable of telling millions of different stories. Between that expectation and the continued online connectivity of players across all mediums of video games, I don't see the modes in any danger whatsoever.
All that said, could we see some changes over time? Sure. Using Madden as an example, maybe Connected Franchise achievements are tied to MUT rewards - for example, if you win the Super Bowl in a CFM, you unlock a John Elway card. This may incentivize those who play CFM to give Ultimate Team a try. Maybe the mode moves away from the dedicated server approach, instead decentralizing and making one player the "host" player and he effectively acts as the server, other players submitting game results to his console and the week-to-week simulations happening locally instead of at some central server bank. What we won't see is the death of online franchise mode altogether.