Hmm, from what I see, you've got a great chance to make a layered game there.
Your battles are looking great, and I'd capitalize on this. Instead of going the mainstream 4X way, perhaps you should focus more on the battles?
4X might only come as a metagame of sorts...
Think, World of Tanks (finite battles) but an added system where how well you behave in a battle (with regards to the resources spent to build ships for example) nets you additional resources / techs to further create new ship components and build larger fleets. There could be some kind of campaign where you must become stronger to attack enemy planets, or you could do it much in the trend of Star Wars Battlefront 2's conquest system where each game 'turn' the enemy moves and you move your fleet(s) and then play each battles individually.
Warhammer 40k Dawn of War I also used something similar in one of its expansion.
There are many topics in your original post. I suggest breaking it down into different threads if possible. I would feel any UI comment I could offer would be out of place in this specific thread that appears to assess the scope of your suggested gameplay.