Many ways of making it work. Many (more) ways of making it not work too.
Let's take examples:
- auto-turrets have a cone of view in front of the turret (20 meters for example).
- so player will make a cluster of auto-turrets for the complete 360° to be covered OR back against a wall. And you got auto-turrets without drawbacks already.
- now imagine you have a player's weapon that reach over 20 meters, so you can get the auto-turret from afar. Then melee class gets avoided as it has just become more limited in its use.
- or devs make as so the auto-turrets cannot be clustered, so you got small "islands" of turrets spread as a minefield instead (gets ugly already).
- or devs restrict the number of turrets, or the way / area they can be built / built on, and players don't feel as free to play as before.
- or devs require the auto-turrets to be powered up one way or another, making it interesting to cut the supply lines rendering those useless, thus making auto-turrets not as useful either.
- or devs request that ammos are to be used in those auto-turrets for them to run instead of power supply and you got a pain in the butt refill line, as it is not as automated as it sounds, and stay a "dumb" AI piloted turret. Meaning you bring the ammo, but will it be really worth it?
- or any combination of the above.
I guess manned turret solve easily all those issues.
1 - it will take some thoughts before building a manned turret: is it well located for defense? Is it easily accessible by us? can the enemy reach it easily? How far is it from what it is defending? Is it worth the resources?
2 - it will take a player out of the battle to use them, thus granting more fire power for example, but restraining troops on the battlefield. Meaning that a smart enemy could choose to bring the battle away from the manned turrets, pushing the defenders out of place, or not depending on how well the defense has been planned.
3 - I would also suggest that manned turrets take ammunition to be used, and nothing else. Meaning that a turret could be handled by only one player if he is willing to bring the ammo, or can also be supported by other players (as active ammo supplier). Meaning more players out of the battlefield, but an enhanced fire power as well.
Manned turret is much more interesting in terms of risk VS reward and strategical decision, that auto-turrets that you try to spread as well as you can, and then never thing about them again.