I believe your suspicions are correct, TheMeInTeam. 2K Games is largely responsible for how Civilization 5 turned out. They did it due to greed, forcing the game to be released far too early (at least a year) as well as thinking they knew better what Civ fans really wanted.
While Soren Johnson could stand up to them, having some pedigree and clout, Jon Shafer was likely taken advantage of and abused by the corporate suits. Budget cuts, creative suggestions that were more aimed at garnering a quick buck rather than retaining long time fans, and the pushing up of the deadline in order to cash in and placate their shareholders led to the debacle of game that we see here now.
The future? The future is bleak and it isn't going to get any better with 2K Games calling the shots.
I generally agree 2K is behind some of the problems, but I think you're giving Shafer too much credit. I mean, this game could have had another year of production on it before release and it still would have some of the huge gameplay flaws we're seeing. 1upt, insane diplomacy, low production values, limited scope, etc. I know 2K and Sid were pushing for an 'accessible game', but Shafer was the one enacting the changes and opening moving it to a Panzer General-style gameplay.
But yeah, the future doesn't look so bright for the series...