Thank you for this feedback.
There is certainly lot's of balance adjustment that will take place. It is the sort of game where changing a 3 to a 5 can make or break the game (and in a game with tends of thousands of values set, that's a lot of balance).
We are constantly in the process of balancing. It happens in every update, it will happen in release, it will happen in every update after release.
And we are always trying to find a happy medium between what is fun and what can be exploited.
The biggest current "exploit" in the game is to play in a large starting sector with no other Ai's near you (so they are all pushed off to other sectors) then overload the map with AI players. They will all be stuffed in sectors with each other, scrapping to get 3-4 good planets each. Meanwhile, the human player has time to expand and colonize 24-30 planets all by himself and can invest in long-term endeavors like colony ships and infrastructure research instead of military.
Even if you set the AI difficulty up high it's still like playing on baby mode.
But, I don't want to take away the ability for players to setup the game however they want to.
To the points expressed here, I want every option to have value in the right situation and if something is so good that it makes other options obsolete, then it's hurting the game. Commanders are great, but are they better than having a governor on a world?
Specific to OP's initial post. He is playing the Hive. The hive gets x3 HP on their ships but their ships don't repair. They are beasts. This means that he's much more open to policies that reduce HP (since he has so much), and they do very well in their initial battles because of the high HP (and less well in future battles as they are more vulnerable to attrition than any other civilization). Their commanders also have the ability to heal if they use Promethion (which is costly for them since their growth rate is based on the amount of stored promethion they have).
I do think there is some better balance that is needed here. Specifically:
1. We will raise the amount of Promethion required to heal them.
2. We will lower their free 20 Promethion (that was added before they got the ability to generate some Promethion per turn on their homeworld).
3. I'm going to play with lowering their HP bonus.
4. I'm going to lower the Missile and Kinetic attack on command ships (the beams looked good). Missiles in particular were really high.