You can say the same about anything complex. I can owned if I don't use any fleet orders. Should I tell everyone that this game sucks? Or that they should remove fleet orders system?
Obviously game will get complex, but it's already complex and people still play it. They can lower the difficulty, they can play random missions. Basically, they are playing it how they want. If the feature is well balanced and documented, it's not a big deal if someone won't use it efficiently. Not everyone is making an ideal fleet composition covering any situation for any encounter.
There is a difference between complexity and depth, and micromanagement. Take MOO3 for example, it's easy to imagine a situation where you have to macro like crazy and yet not contain much depth at all. SotS being the example raised. There's really only one way to manage trade routes well in that game, but you're stuck doing things that a computer should be doing.
Likewise in MoO 3. Most of the player time during the end game is spent managing all the planets of which a computer could have been told to do, and it would seem many people would have liked the computer to do it if the response to that part of the game is anything to go by.
This isn't about whether or not the developer should make the game complex or not, but whether it would be justified or not to implement automation where player input can take place. Take into consideration that there's a fair bit of automation in place already. Unlike an RTS, the AI in this is is quite complex, far more complex than in games like starcraft or SPAZ at the individual level of the unit. For example, you can't manually kite an opponent like in starcraft with a vulture, but the AI in this game already does that for you, and as often the case done against you as well. This is a good thing when it is justified, and given that the game is aimed at putting your character as a character who has to command his fleet but more importantly command his ship as well, I think it is justified.