Ol' Turncoat has failed to explain how Johnny's strengths mesh better with a dominant running game as opposed to Hoyer's strengths.
If Hoyer is an under center game manager with decent athleticism, a la an Alex Smith type, play action off the run works just fine off his strengths. Johnny might have a better deep ball but he isn't connecting to receivers in either the 1st or 2nd team offense.
It's just the nature of a power run, spread offense. Mobile QB's have an advantage out of the pocket when they can fake a dive into the LOS. It freezes line-backers and safeties, allowing mobile QB's to get the edge on run/throw options. It's why guys like RGIII, Colin Kapernick, and even Brxaton Miller at Ohio State are so successful. The threat of the mobile QB can also loosen up the defense in the middle as interior lineman, middle linebackers, and safeties all need to account for the edge.
While in a standard power run game, play-action is a staple and can be very successful, we just don't see it a ton anymore. Even prototypical pocket QB's like Peyton Manning, Tom Brady, and Drew Brees are involved in spread offenses. Kyle Shannahan will likely be more well versed in an offense suited to Manziel than Hoyer, IMO. If Manziel is even close to Hoyer coming out of camp (which he may not be) I still think Manziel probably gets a crack because there is a lot more you can do with him, and he puts more pressure on a defense with his versatility.
There's also a huge concern in our wide-receiver make-up but this is a bit deeper down the rabbit-hole. With the lack of explosiveness without Josh Gordon for likely a long time, the limited capabilities of our guys on the outside is problematic. Even if you freeze a safety over the top, you need receivers that can create separation and make catches down-field in a precision passing game. My point being, even if you get the run game going and start attacking the secondary as they cheat to stop the run, without the talent at the WR position, you may not be able to exploit soft spots in a defense on play-action because of lack of separation. In a power-run game spread, called plays, audibles, and reading and reacting to the defense is less about precision but more about weaknesses in the defense and where they are vulnerable. It's why guys like Tebow, Braxton Miller, and RGIII did and do excel. Decisions are largely made for you and it's one, two reads at the most. Less about reading a defense and more about executing the designed play-call where X's & O's by the staff have essentially made the read for you.
I'm interested to see how it plays out. I do think a power-run game spread with Tate, West, and Crowell would be really fun to watch with Manziel at QB, assuming he can limit turnovers (which so far hasn't been his M.O.). I also think Cameron Jordan will be a monster in a Kyle Shanahan offense, especially if defenses have to account for Manziel's mobility. That's a ton of pressure on safeties and OLB's.