Alcantara isn't playing every single game in CF. He's played 10 games out of 86 games. If he were as guaranteed to play there as you're suggesting he would be playing there daily. He's not even playing the majority of his time there recently. Additionally, it's not like they didn't see this coming. We've known since Bryant was drafted that there was going to be a logjam of players in the infield. So, if it was a certainty they would have moved him to CF then instead of having him hang around at SS until Baez was called up to AA last year and forced him to move to 2B. Also, if that was the move why move him to 2B in the first place? Go straight to CF.
Why isn't Baez getting time at 3B? Perhaps because Bryant is still playing there and Villanueva before him. As for why Bryant isn't moved, that's because they want to see him at 3B as long as possible. And the flip side of your argument is if Baez is certainly going to 2B then why isn't he playing there full time right now in AAA? You make it out like switching from SS to 3B is some epic change. Manny Machado played a grand total of 4 games there before starting an entire season there a few years back. And Machado has been pretty good there. In 51 games in 2012 he had a UZR/150 of 5.3. Last year at 3B he won a gold glove with a 31.2 UZR/150.
Whether or not Baez likes it is pretty irrelevant. He'll play where they put him. Am I guaranteeing that's where Baez will play, of course not. However, I think it makes the most sense. Additionally, with Castro/Russell at SS and Baez at 2B you leave yourself very little room to add 1/2 hitters. Typically, you're talking about table setters coming out of CF, SS, and 2B and two of those will be taking by players who are unlikely to hit 1/2. Perhaps you can argue Russell can hit 2nd and Alcantara/Almora can lead off but that doesn't leave you much wiggle room. And maybe you can add a lead off hitter out of LF or RF but at that point you're removing Soler/Schwarber types from corner outfield. By playing Alcantara at 2B, it gives you two common positions for top of the order hitters even if Almora and him end up failing.
Like I said, Baez profiles more as a 3B than a 2B because of his power. Can he play 2B? Yeah probably but can you find a lead off hitter type as a 3B/RF? That's harder.