Will state clearly that I do like this game, this is to highlight what I consider issues. This is all my opinion (obviously) and is NOT meant as an attack.
No ability to set a constant steam of rotating production. If I want transport then marauder unit I need to keep plug it back in when it clears. A rotating que would be set and forget.
Ship formations (a big issue for humans especially due to the slow speed of their heavy cruisers). Since you cannot overlap ships, and cannot set ship placement at the start of a battle you wind up with your fast hulls stuck behind your slow hulls, or worse your ground force transports mixed in with your space combat units ( I tend to skip heavy cruiser production entirely and use assault cruisers mounting fighter bays since assault cruisers actually have a viable space speed, but these ships actually get placed BEHIND carriers which I use as assault shuttle deployment vessels) There should be a way to denote where a ship belongs in your order of battle (set during design or refit, perhaps a 1 to 5 scale, 1 front of the line, 5 in the baggage train with the transports.)
Cannot produce military hulls with *empty* assault shuttle bays. If I want to field marauder units as gremak I need build transports to do this, since an assault bay comes preloaded with an armor unit. If I am metal poor I would even prefer to use planetary population at times, also not an option because the bay comes preloaded, (perhaps an empty / full option similar to civilian freighter / troopship designs?)...
Computer player can see exactly what military power you have, while their information remains hidden from you. War is declared based on military might, not taking anything else into account.
Terraforming needs to give some sort of preview as to what it will do (will I have overcrowding issues).
Some homeworlds can be terraformed (gremak), some cannot (yoral)