Combat in Civ takes up hundreds of thousands of lines of code and was developed by a huge dev team.
Zarksoft is a very small team and they are trying to improve the game based on our feedback, just saying "do what someone else did" is not helpful unless you are gong to provide some examples of how it can be implemented here.
As for what we can do to improve the system, I like atk speed mainly because it adds a different variable that can be used to differentiate the ships. Also I think random assignment is a bad idea as it makes it very easy to exploit the system such as the previously mentioned probe spam tactic.
One way to do it would be for Ships to target ships of the same class first, then the largest ship/target, then orbitals, then planets.
This prevents using worthless units to make larger ones invincible but still provides value for having escorts and makes atk speed a useful stat. Thus having escorts protects your capital ships from being swarmed by smaller ships. Which is exactly the role such ships play in actual warfare.
I like the idea of giving players a reason to have a mixture of ships as opposed to just building fleets of 200+ Dreads. but i definitely dont want to see fleets with 500 probes wandering around.