I'm pretty sure that for any real-life tank, you'd only ever want to have gun, because you need the accuracy when shooting at other tanks and stuff. This is even a problem in APB where you have to adjust your aim between the two shots when you're in a heavy or Mammoth tank, but in a Medium tank you can just hold the gun steady in place. Whereas when you're a big cruiser or battleship, you're shooting at other big cruisers or battleships, so having multiple guns on each turret makes more sense.
As for missiles, I don't think there'a any real-life situation where'd you want to use guided missiles against infantry (missiles are expensive and I don't think there's any homing mechanism to target people), especially when you can just fire HE shells. So that just leaves the anti-aircraft function...I think there's some tanks that can fire AA missiles out of their main guns, but I don't know how common that is. AA weapons are kinda delicate and fragile, so you probably want them mounted on separate vehicles rather than on main battle tanks (just like in real life!).
And lastly, once your tank gets to a certain size, there's just no way you can put enough armor on it to protect the whole thing. And your enemy will just build a bigger anti-tank missile.