To cut to the chase:

The way ships fight is very unintelligent (or at least appears to be). For example, weapon ranges and the advantages a ship with range advantage should get, from what I can tell, have very little effect. For example, a ship with long range missile weapons should be attempting to engage at long range and then attempt to hold the range open and get as many shots off outside of the enemy's weapon range. Not dive in and get blasted to pieces by enemy short range beam weapons for example. (Sure if the missile ship lacks the speed to keep out of range, that is a different story).

This shortcoming seems particularly acute when an inferior force with long range weapons should effectively be fighting a retrograde action to get away/keep the range open as long as possible.

I'm fine not having tactical control of the ships, but not so much if the ships fight "dumb". Failing much better tactical play, at least having the ability to pause the action and issue orders to ships doing stupid things (open range, close range, etc.) would go a long way.

Of course, an optional full blown tactical game (like Age of Wonders III) would be great too.